This may be caused by not having cr/lf (0d0a) terminated lines in the .mas in windows but just cr (0d) being present

Might happen when you transfer master files from unix to pc.
The other way around (from pc to unix) may also lead to strange results, every line will then be ended with cr/lf while unix only needs and interprets one of them. The other one is passed on to focus, leading to all kinds of strange results.