Just a warning - I think this was caused by a PYPN script error:
I just did an undo that reset my file to a state from 2 days ago and caused me to loose a large block of (tested) programming. Of course as Murphy would have it this code was particularly painful to develop the first time and is turning out to be a pain to recreate.
I don't have time at the moment to really investigate the cause but I *think* it may be caused by a PYPN script beginning an undo action and then not ending it.
What confuses me is I though that once you save a file you can't undo back before that point -- but in the newer version I guess you can. So just a warning to look over your file before you save! Close and reopen the file every now and then. Be careful with you code! :(