Can't say I've hit the same problem. Where are you seeing this IRQ conflict alerted? Or is it just mentioned when you are in System Information? In which case, my experience with shared resources is that this isn't such a big deal and IRQ chains are almost something Windows 2000 onwards encourages.
If it is a problem, something in your BIOS settings (or CMOS data save area) may have altered or become reset to defaults.
So, am interested in where you are seeing this please, Waggs?