.ape is only supported in windows, iirc. flac or shn will work on just about every OS.
My suggestions to you would be, in this order:
1) checkout the help forum over at
http://forums.etree.org and see if somebody has a quick fix for your problem. shn is still the most commonly used lossless audio compression format, don't give up on it so easilly.
2) download and use flac.
http://mikewren.com/flac/ has a quick installer that includes a frontend GUI interface to make working with flac files very easy.
I basically wrote off .ape a while back when there were no plans to make it useful on non-m$ operating systems. I now see that a linux port is in the works, and that the source code is available. I'd guess that a Mac version would be available soon then as well, but until then, I'd really suggest sticking with shn or flac for their cross-platform support.