With Autorun off and the "$recycle.bin" and "System Volume information" folders deleted, it still causes a BSOD when the USB enclosure is added to the Windows machine.

I hooked it back up to the Linux DiskStation, shared it, and mapped the network drive onto my Windows box to grab a copy of my most critical files, and I am now Virus scanning the entire mapped drive. Assuming that finds nothing (which I highly anticipate that it will) I will look at the other partition on the drive, which Linux mounts separately; that partition is bootable so maybe something in it is causing windows to throw up all of the sudden....even though I am not booting from it .