Malwarebytes, Spybot and Ad-aware are normally used in a run on demand basis, so no conflict should be occurring. But I suspect some might have an option that says to load and continually protect. Maybe you should check what you are running on boot-up and disable anything you didn't intend to run.
However i note that none of these were able to fix the problem, which is interesting. You sure this is the case ? If you still have a problem it may be the virus you found causing the delayed start. Or maybe you never had one and your PC has a different issue.
What you can try is booting into 'safe mode' to check things out. Failing that booting off a disk might allow you to investigate the problem easier.