How do I avoid having a ";1" on my ISO-9660 discs?

The ISO-9660 standard says the version number (a semicolon followed by a number at the end of every filename) has to be there. Most operating systems simply ignore it, but until recently the Mac didn't, causing some problems.
(For the Mac, look at "ISO 9660 File Access" in the System:Extensions folder with Command-I. If the version shown is 5.0 or greater, your system should handle the version numbers just fine. If not, you should update your system software.)
If you can't find a way to work around it, "mkisofs" has an option to omit the version number when constructing an ISO-9660 image.