Check your Device Manager,  Event Viewer. You can probably detect what it is by running this command:

msconfig 

Go to Startups. If you have any devices (eg Iomega) checked, uncheck it/Apply/OK/Restart. 

I'll assume your system is reasonably new and you've checked your Device Drivers. You've patched any running software, checked logs, have no conflicts with security programs, ran sfc and msinfo32, checked Program Files folder and uninstalled any programs that don't come with any other uninstaller (if you know what you're doing) ? The only software that's been mentioned is Spysweeper and (XP's ?) Flash Card Reader; uninstalling/regediting one/both of these may do it but it's a long shot. Let us know how it goes.