WinME does not have the ACPI functionality that Win2k does. Win2k provides an entire hardware abstraction layer between the OS and the IRQs for cards. They are completely different OSs and WinME doesn't have the slowdown or the benefits from this.
If you do have hardware sharing IRQs in WinME then you have to either assign cards different IRQs through the BIOS or Windows, or you have to move them to different slots so they get assigned different numbered IRQs.