A Q6600 should be way more than enough power for MC. Assuming you have adequate RAM, it should "scream" on that system. Can you do a favor and post the system info for us? Go to the Help Menu in MC and choose System Info, then come here and paste the contents (it auto-copies it for you).
Some other questions...
1. I know you said you disabled it, but which specific Anti-Virus application are you using?
To explain: Anti-virus applications can slow down MC because, by design, they run a quick scan of every single file before it is accessed. MC expects and needs near-instant access to it's database files. One thing that can help is to exclude the database location from the Anti-Virus search. The way you accomplish this varies in different A/V apps, but if you use the default database (library) location in MC, the folder you need to exclude is:
c:\Documents and Settings\<YOUR_USERNAME>\Application Data\J River\Media Center 12\Library2. Auto-import shouldn't slow the machine down significantly (I run all my machines with it enabled), even with remote network drives and USB drives, unless it is busy building thumbnails for video files. If you're using a SATA connected drive, you should be fine, assuming the drive is working properly and at full speed. One suggestion... Try manually building your thumbnails overnight. MC can sometimes slow down substantially when it is building thumbnails on the fly. To do this, go to:
Tools --> Options --> Tree & View --> Thumbnails --> Build missing thumbnails. This will take a while, so start it and go to bed.
3. I'm suspicious of disk or memory access problems on that machine. What motherboard does it have? Are you sure you've installed the latest Intel Chipset drivers (assuming it is an Intel chipset on the board)? You can download these drivers for all boards that use Intel chipsets here:
http://downloadcenter.intel.com/If you aren't sure you have them, it won't hurt to download and install the latest drivers. I can help you find the exact right ones if you tell me what motherboard you have. If you aren't sure,
download CPU-Z and use it to identify the board and chipset.
If you are running without chipset drivers installed, your machine could be running the SATA drives in "legacy" mode, which can be incredibly slow. You also would be running without the full benefit of your faster memory access and everything else in the system.
4. If you're sure you have the right drivers...
Download HD Tach and run the Long bench on your system and media drives. Report the results here and we can compare them to known-good results.