I set up a new system 2 months ago (mobo+cpu+ram+gpu). Fresh install of w8.1 with drivers from manufacturer install disk. I started getting huge lag spikes, which appear mostly when dragging windows around on the desktop or wiggling the cursor around. Basically the whole system just halts for 0,5-1 seconds. Also happens mkv playback, browsing etc, but most notably when moving the cursor.
I thought I messed up with the installation of windows so I reinstalled it again. No help there, so I started going through things that could be causing it, mainly bios settings, mobo drivers and various windows settings. Especially the management engine driver and HPET timer forcing/disabling. I thought I had it fixed for about 5 weeks, which it worked perfectly.
Couple weeks ago I upgraded my cpu. The system was 100% stable with 4,3ghz cpu overclock and some gpu overclock, IBT very hard passes, some tough memtests and 30 hours of Dying Light without any problems. Everything was fine until I needed to fix a non-related mobo network driver memory leak. Just a simple registry fix to stop network monitoring at system startup, but I also ran ccCleaner. After this the problems started again and its unbearable.
Mouse movement: I've used 3 mouses and the ones with high polling cause the worst problems. With 500hz/1000hz the interrupts become apparent eg. full second halts, but with 125hz settings its not that apparent. The latency is lower, but still there are problems, low fps in games for example and infrequent and varied BSOD's. I use windows' own drivers for mice. When I installed logitech gaming center drivers the computer started bsoding 10 seconds after every boot, so had to roll back. Also, according to mouserate.exe it seems that I cannot activate 1000hz in zowie, only 500hz. But if do it anyways, the problems are far less, than at 500hz setting even if reported rate is around the same. G400 reports 1000hz, mx300 reports 125hz.
System settings: I know the problem has to do with the system clock/syncing rate somehow. The system halts happen when the processor is changing power saving state and frequency (800-2100-3500-3900mhz). If I disable EIST I will not get any halts, just like when I use a lower polling rate mouse, but the problem persist (low fps, bsod's). Overclocking/stock does not affect the problem, nor do the power saving states (apart from eist, but not really a fix). I haven't even tried disable HT, because it has worked before and the pentium did not even have HT and still had problems.
Drivers: The final culprit for the latency is wdf01000.sys, but I don't think it can be updated. I also don't think it's the one causing the problems, because why would it suddenly break when it hasn't been modified. There was an automatic intel management engine update 2 days ago, at the same time as the problems started. I thought it was that causing it and did the update from windows update. I think it might have helped for like 1 reboot and then stuttering again. I've tried every management engine driver I can find, there's no difference. Even without a driver it stutters. I've tried enabling/disabling HPET (forced on and apparent in device manager by mobo, cannot disable) again, no results there either. Bios has been updated twice. As a last resort used TweakBit Driver Updater, the program did update a couple of the essential drivers, but it didn't help either.
Basically the system has been doing this error from a 2 hour old fresh windows install and also now in a 2 month old, so I believe I have not messed up anything. If I can manage it, I will refrain from reinstalling windows, because already did it and did not help. So here i am. 10 points to you if you read the whole thing. Now please help?
GigaByte z97x-gaming 3
i7-4770k (g3258 anniversary), proper cooling
Crucial Ballistix sport 1600 2x4gb
GTX 670 (Gtx 470)
Corsair TX750
Zowie FK1 (G400, mx300)
Samsung display 22"@ 120hz (60hz, no difference)

I thought I messed up with the installation of windows so I reinstalled it again. No help there, so I started going through things that could be causing it, mainly bios settings, mobo drivers and various windows settings. Especially the management engine driver and HPET timer forcing/disabling. I thought I had it fixed for about 5 weeks, which it worked perfectly.
Couple weeks ago I upgraded my cpu. The system was 100% stable with 4,3ghz cpu overclock and some gpu overclock, IBT very hard passes, some tough memtests and 30 hours of Dying Light without any problems. Everything was fine until I needed to fix a non-related mobo network driver memory leak. Just a simple registry fix to stop network monitoring at system startup, but I also ran ccCleaner. After this the problems started again and its unbearable.
Mouse movement: I've used 3 mouses and the ones with high polling cause the worst problems. With 500hz/1000hz the interrupts become apparent eg. full second halts, but with 125hz settings its not that apparent. The latency is lower, but still there are problems, low fps in games for example and infrequent and varied BSOD's. I use windows' own drivers for mice. When I installed logitech gaming center drivers the computer started bsoding 10 seconds after every boot, so had to roll back. Also, according to mouserate.exe it seems that I cannot activate 1000hz in zowie, only 500hz. But if do it anyways, the problems are far less, than at 500hz setting even if reported rate is around the same. G400 reports 1000hz, mx300 reports 125hz.
System settings: I know the problem has to do with the system clock/syncing rate somehow. The system halts happen when the processor is changing power saving state and frequency (800-2100-3500-3900mhz). If I disable EIST I will not get any halts, just like when I use a lower polling rate mouse, but the problem persist (low fps, bsod's). Overclocking/stock does not affect the problem, nor do the power saving states (apart from eist, but not really a fix). I haven't even tried disable HT, because it has worked before and the pentium did not even have HT and still had problems.
Drivers: The final culprit for the latency is wdf01000.sys, but I don't think it can be updated. I also don't think it's the one causing the problems, because why would it suddenly break when it hasn't been modified. There was an automatic intel management engine update 2 days ago, at the same time as the problems started. I thought it was that causing it and did the update from windows update. I think it might have helped for like 1 reboot and then stuttering again. I've tried every management engine driver I can find, there's no difference. Even without a driver it stutters. I've tried enabling/disabling HPET (forced on and apparent in device manager by mobo, cannot disable) again, no results there either. Bios has been updated twice. As a last resort used TweakBit Driver Updater, the program did update a couple of the essential drivers, but it didn't help either.
Basically the system has been doing this error from a 2 hour old fresh windows install and also now in a 2 month old, so I believe I have not messed up anything. If I can manage it, I will refrain from reinstalling windows, because already did it and did not help. So here i am. 10 points to you if you read the whole thing. Now please help?

GigaByte z97x-gaming 3
i7-4770k (g3258 anniversary), proper cooling
Crucial Ballistix sport 1600 2x4gb
GTX 670 (Gtx 470)
Corsair TX750
Zowie FK1 (G400, mx300)
Samsung display 22"@ 120hz (60hz, no difference)
