If your having trouble with it not being able to read a file, a DLL or something, it has something to do with the 200mb partition that is included in your partition table when you boot from a windows install.
Personally, I always took it out, leaving just the NTFS (or FAT32) Windows partition and the MAC partition and it always worked fine for me. The only difference is that if you ever decide to change the partition table, for example back to one MAC partition, you would have to reinstall Leopard and use disk utility to reformat your hard drive.
It's a workaround, but kind of a pain, I had the same trouble a while back.