I have a vintage 2003 XP box Intel motherboard with an Intel P4 motherboard. It's needed periodic brain surgery but I make as few changes as possible. This is geriatric computing -- don't mess with things that work.
The most persistent annoyance I've had came when I moved to 1TB external drives for backup:
Briefly, I had to disable "legacy USB" support. Once that was done the system starts normally. I spotted this by turning on the BIOS settings to show all startup messages and do a full (slow) startup -- I could see it was hanging at a USB step just after checking the keyboard.
Since I was in the BIOS I made a few other incidental changes. I no longer use Serial or Parallel ports (yeah, old machine) so I disabled those. I also told the BIOS to use PnP (which I see I also did in 2003 so it looks like I reset the BIOS back to defaults sometime in the past six years).