Chkdsk Results In Unusable System w/o Restart

[keLston]

So i'm having this really weird issue lately and i'm not sure what's causing it. It seems to cause no long term problems (i've had this happen for months now), but it is really annoying.

Using Vista 64's built in check disk problem (with automatically fix errors checked), once it goes through the check and I log into Windows, the system is pretty much unusable. A select few programs will start (like O&O Defrag will start) but most programs won't start nor will most startup stuff, like Firefox or Internet Explorer will not load after the initial boot up after a chkdsk. Windows Explorer won't even start (win key + E) and all I can really do is reboot. When I reboot, everything is back to normal but it's really annoying to have to reboot 3 times every time I do a chkdsk.

Did a full surface scan and everything and there's no problems being reported for the hard drives.

Intel C2D 6850
4GB Ram
Asus Striker Extreme
evga 8800GTX
X-Fi Fatal1ty
2x 750GB Western Digitals (WD7500AAKS)
Vista 64 with the Service pack + all updates