The transparecy issue goes back at least 2-4 months and is a bug that Topaz never fixed. I first found it with GigaPixel, where it showed as a problem first with PNG files that had transparency. Not all files had this problem, only some, for no known reason.
I had already isolated the problme to the step that writes the processed file to the output because the preview looks correct and the GigaPix program crashed just prior to writing the output file. This was confirmed by Tech Support.
I have since reported it to Tech Support and they were able to duplicate the problem, but never solved it. Prior to leaving he found a workaround to the PNG issue. This was to request a file conversions to TIFF instead of keeping it PNG. This worked really well. However, with the next update, the TIFF workaround stopped working and made the transparent regions opaque. Now every update beta or otherwise now has this BUG.
Unfortunately the Tech Support person who took this seriously and who duplicated it left so there is no one else working on this. I opened the ticket again, which is how I found it that the Tech Support fellow had left but no one had picked up on the unfinished problem and after several months never heard from Tech Support I sent a query about a week ago and still no response.
The most important message however is this:
This bug appears to be in every AI program (not Mask AI of course). Had someone fixed it right when it first appeared, it would have caused less confusion and frustration. Of course the fact that not all PNG and TIFF files have the problem makes it much more difficult to solve.
So if you have a file that fails to work, please open a Ticket and submit your errant file.