That could be the issue. The files were generated on windows and will have windows-style line ending markers, which doesn't have to be a problem if gmod handles it but knowing garry he probably didn't do anything about that for the linux build of gmod. You'll have to modify the scripts to use linux-style line endings.
If you have shell access on the linux box, you could navigate to where the scripts are and run:
dos2unix *.txt
That will convert all scripts to linux-style line endings.
I think the dos2unix/unix2dos utilities are standard on all linux distros. An alternative is using an editor like notepad++ to convert them (Edit -> EOL Conversion -> Unix format). Most text editors that are a step above basic notepad will have a function like that.