I think the assembler format accepted by as is a bit different from that accepted by PhxAss. Also, the GNU linker needs a.out format object files as input, whereas PhxAss generates Amiga-native hunk format files. I don't know if there's any solution to this problem. Not accepting hunk files has been one of the main problems with Amiga GCC for a long time.
If you still have problems with comments, apparently gcc accepts C++ comments as long as -ansi or -traditional aren't used.
