Hi,
I had a similar problem with "GnomeBaker" (the default CD burner app with Ubuntu Linux).
I solved the problem the other way round - have you tried
AmiCDFS on your Amiga?
It works well with standard ISO9660 (both standard and with RockRidge extensions), Macintosh HFS, hybrid CDs, audio CDs, etc... Seems much better than the standard CD filing system supplied with OS3.9.
- Ali
