McAfee checks a bunch of files on start up as scanning all files that are loading into memory (as any anti-virus program does). Any anti-virus program will take a hit on your system performance, but it shouldn't stop everything wholesale.
The problem is likely the same problem everyone else has with McAfee: it just plain sucks. Starting with version 5, they revamped the product for Win2k and when they did, they screwed it up royally. Sucked the life out of every machine I put it on. Switched to Norton Anti-Virus and it has worked really well for me for years without taking a serious hit on performance.
My 2 cents.
Try uninstalling McAfee and see if your performance improves dramatically. Then you'll know if it is McAfee or something else. But it's probably McAfee.
I am a computer reseller and I see many people with problems with McAfee.. I recommend uninstalling it and getting Norton Antivirus.. you can also set some options to tell NAV not to scan files when 'run or opened' which will save some time..