I have used RailModeler Pro on my Mac - though its been a while. I recall having a couple of issues with the software (I really don't recall exactly what it was - I'd have to dig way back into some old emails to try to suss it out) and the folks at http://www.IsleOfTheKakapo.com (the developers) were very helpful. If you haven't already, you might try contacting them via this link and see if you can get them to resolve the problem - it sounds like its a more generic issue that just something you are doing.
RailModeler is really the only layout planning software I've used - likely because its built for the Mac - so I can't really compare to other track planning software. They've added a lot of bells and whistles to it - and there's always the advantage (at least most of the time) of being familiar with the software as opposed to learning something new.
