I had/have a similar problem: burning Unix files to a CD writer attached to a Win 2000 server. We use Samba to connect to the Unix servers.
The first CD software I used, even though I specified ISO and long filenames, resulted in a CD with long filenames that were OK when viewed on the Win server, but when the CD was mounted onto a Unix server, the tilde (~) was thrown into the long filenames. Unix couldn't use the CD.
So, I got a tip from one of these Tek-Tip forums about using Nero CD burning software. This was better: the long filenames stay long when the CD is mounted on Unix.
One problem remains, however: the files I am burning to the CD ROM are compressed files, with the .Z final extension. For some strange reason, the CD burning software changes the .Z to a .z (even though it appears as a .Z in Windows).
So, once I get the files from the CD into the Unix directories, I have to run a script (created with the help of yet another Tek-Tips forum!) to change the .z to a .Z. That's a small problem I can live with.
I'm beginning to think the only solution is to get a CD burner and attach it to a Unix system and do the burning from Unix.
You can get a trial version of Nero from the Web. It might help in your situation.