Ameraves
Obviously... Ignore what follows if you've already decided to re-install Windows. =)
These two statements seem to contradict each other, yet I believe what happened was... changing the BIOS screen mode just allowed the Windows loading screen to appear, when for some reason before it was being hidden. (I had something like this happen years ago, in my case I got a black screen, and my desktop would appear magically later on.)
So I don't think you have a BIOS/Boot/Hardware issue at all. I think it's purely Windows dragging the chain. No POST errors, no "OS not found", no hard lockups requiring a reset. I just can't see a reason for a machine to stop for 3+ minutes, BEFORE Windows even begins loading, and THEN continue every time to the desktop.
Create a new text file on your desktop e.g. "Clearlogs.cmd" - Edit and insert these 2 lines:
FOR /F "tokens=*" %%1 IN ('wevtutil.exe el') DO wevtutil.exe cl "%%1"
pause
Run this batch file (as Admin or you will get pages of access denied errors) and it will completely nuke your event logs. Reboot and Windows will have a fresh set of logs for you to inspect just for that restart. I'm kinda interested to see what the culprit is.