There are usually a few options in BIOS relating to USB devices. One should cover whether or not to attempt to boot from USB devices and another may pertain to the handling of legacy USB devices. I know my mother's old Lexmark all-in-one would cause her boot to hang for a significant amount of time due to the fact it had a memory card reader built in, and the BIOS of the computer was timing out on the card reader, trying to boot from it. Turning those features off in BIOS didn't affect her computer usage at all, but it sure sped up her boot process.
You may want to have a look into the options available in your computer's BIOS to see what you can find.