Chkdsk finds errors every time I run it [Slow Boot Time]

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Okay, so everytime I run Chkdsk it always finds errors on the disk. I am unsure why, but if I run chkdsk back to back, it will keep constantly find new errors every time. Also, the Chkdsk takes about 2 and a half hours to complete, and always gets stuck at 10% for most of that time. [I run Chkdsk /f /r, it reboots the computer and runs]

This is what I have tried so far:
1) Running SFC /SCANNOW. It has fixed errors in the past used alongwith DISM. I just ran SFC again to be sure, no errors found.
2) Checking computer for malware. I have Malwarebytes Pro and Bitdefender Pro. I seriously doubt malware caused this since I have at most found 5 minor threats on my computer in the past year. Just to be sure, I ran a few scans in safe mode with Malwarebytes, and Hitman Pro, etc. All clean.

More Info on my problem:
The reason why I found out about the Chkdsk problem is because my computer has started booting up slow. About 2 weeks ago my computer would take 10 seconds to go from POST to login screen. Now it takes over 75 seconds [With Windows 8 Fast Start up Enabled]. I began investigating why, with no apparent reason. No big start up items, nothing running at start up that shouldn't be there.

Lately, I have been reading Errors and Warnings in Event Viewer as an idea to figure if anything was wrong. I have dealt with a few errors individually, but no improvement.

Here is some Info on programs I use on my computer.
1) Malwarebytes PRO [In Startup]
2) Bitdefender Total Security 2015 [In Startup]
3) Driver Booster 2 PRO - I use this to update my drivers, never had any problems with it. [Should I keep it?][Disabled from Startup]
4) Wise Care 365 - A suite I got, it has many helpful tools I use. [Should I keep it?][Disabled from Startup, except boot time tracker]
5) AOMEI Partition Assistant PRO - I ran a full check on my Hard Drive for bad sectors with this, nothing found.[Disabled from Startup]
6) SpywareBlaster[Not in Startup]

If you need any more info, please reply. I have tried everything I can think of, and need some help from someone.

Thanks!

EDIT: System Specs

ACER - Windows 8.1 Home Premium 64 Bit Desktop
Intel Core i5 3.1Gz
8 GB RAM

Forgot to add, most recently I went into safe mode and ran "Chkdsk". It scanned and told me "Windows has checked the file system and found problems" "Please run chkdsk /scan to find the problems and queue them for repair". I ran "chkdsk /scan", and got this message: "A snapshot error has occured while scanning this drive. Run an offline scan and fix".
 

My Computer

System One

  • OS
    Windows 8 Home Premium
    Computer type
    PC/Desktop
What make of hard drive? Best to run their drive checking tool if they have one. Does SMART show anything bad especially high reallocated sector count?
 

My Computer

System One

  • OS
    Windows 8.1 Pro 64-bit
    Computer type
    Laptop
    System Manufacturer/Model
    Acer V3 771G-6443
    CPU
    i5-3230m
    Motherboard
    Acer VA70_HC (U3E1)
    Memory
    8GB DDR3 PC3-12800 (800 MHz)
    Graphics Card(s)
    HD4000 + GeForce GT 730M
    Sound Card
    Realtek High Definition Audio
    Monitor(s) Displays
    17" Generic PnP Display on Intel HD Graphics 4000
    Screen Resolution
    1600x900 pixels
    Hard Drives
    Samsung SSD 850 EVO 250 GB
    ADATA SSD SP900 128GB
    PSU
    90 watt brick
    Mouse
    Bluetooth
    Antivirus
    Comodo
    Other Info
    Asus RT-AC56R dual-band WRT router (Merlin firmware). Intel 7260.HMWWB.R dual-band ac wireless adapter.
Western Digital WD10EZEX-21M2NA0 (1000GB)

What is SMART and how do I check it?

I'll go look for a tool for my Western Digital also.
 

My Computer

System One

  • OS
    Windows 8 Home Premium
    Computer type
    PC/Desktop
Okay I found my Hard Drive on their website and I am beginning a test with "Western Digital Data Lifeguard". I am going to do a quick diagnostic, and if nothing is found I will try the extended one. I'll be back soon.
 

My Computer

System One

  • OS
    Windows 8 Home Premium
    Computer type
    PC/Desktop
Ran the quick and full diagnostic. It said my hard drive "PASSED". Back to the drawing board...
 

My Computer

System One

  • OS
    Windows 8 Home Premium
    Computer type
    PC/Desktop
I noticed you have both Malwarebyte Pro and Bitdefender. First not sure you need both in the first place but definitely would not have both running at startup. Yo do appear to have many system intensive things loading at startup, try disabling them one by one or all at once then renabling one at a time.
 

My Computer

System One

  • OS
    Windows 8.1 Pro 64-bit
    Computer type
    Laptop
    System Manufacturer/Model
    Acer V3 771G-6443
    CPU
    i5-3230m
    Motherboard
    Acer VA70_HC (U3E1)
    Memory
    8GB DDR3 PC3-12800 (800 MHz)
    Graphics Card(s)
    HD4000 + GeForce GT 730M
    Sound Card
    Realtek High Definition Audio
    Monitor(s) Displays
    17" Generic PnP Display on Intel HD Graphics 4000
    Screen Resolution
    1600x900 pixels
    Hard Drives
    Samsung SSD 850 EVO 250 GB
    ADATA SSD SP900 128GB
    PSU
    90 watt brick
    Mouse
    Bluetooth
    Antivirus
    Comodo
    Other Info
    Asus RT-AC56R dual-band WRT router (Merlin firmware). Intel 7260.HMWWB.R dual-band ac wireless adapter.
I think I do need both, Malwarebytes says it works alongside an Antivirus flawlessly to provide complete protection.

In good news, I think the Hard Drive Fixing Utility actually did some good. I booted my computer up this morning to find it taking the normal 15 seconds. Evidentally the extensive test did fix some issues.

So i'll say: SOLVED! Thanks to Popeye, and "Western Digital Data Lifeguard" :)

I'll post back if the issue comes back, and I will look into what you said about the start up items popeye.

Thanks again!
 

My Computer

System One

  • OS
    Windows 8 Home Premium
    Computer type
    PC/Desktop
Good news! :)
 

My Computer

System One

  • OS
    Windows 8.1 Pro 64-bit
    Computer type
    Laptop
    System Manufacturer/Model
    Acer V3 771G-6443
    CPU
    i5-3230m
    Motherboard
    Acer VA70_HC (U3E1)
    Memory
    8GB DDR3 PC3-12800 (800 MHz)
    Graphics Card(s)
    HD4000 + GeForce GT 730M
    Sound Card
    Realtek High Definition Audio
    Monitor(s) Displays
    17" Generic PnP Display on Intel HD Graphics 4000
    Screen Resolution
    1600x900 pixels
    Hard Drives
    Samsung SSD 850 EVO 250 GB
    ADATA SSD SP900 128GB
    PSU
    90 watt brick
    Mouse
    Bluetooth
    Antivirus
    Comodo
    Other Info
    Asus RT-AC56R dual-band WRT router (Merlin firmware). Intel 7260.HMWWB.R dual-band ac wireless adapter.
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