I'm an animator and I use XPGD a lot for creating .swf assets(non -animating). I can't say I have encountered the problems that you have. The one big thing to note is that if you have profiled lines in Xara it is best to change them to editable shapes.

The only suggestion I have, based on my experience with Adobe and Flash updates, is that it may well be Flash that is the problem. I have Flash CS3 and it seems to work fine. Maybe it is CS4 that is the problem?
If you want to post a bit of a demo xar file I can see if I can export and open it in CS3 if you don't have it?