Sorry I didn't respond earlier, but I'm happy to report that the waypoint problem I reported is not an issue with 2.0. I see that in the new version, cache waypoints and user waypoints reside under different list headings, but all of them are there when I look for them. In fact, I was a little surprised to find that not only were the user waypoints I had just saved now properly displayed, but it also showed the ones I had saved days before. So I see what you mean when you say that the PQ downloads come with more information than before! Anyway, all seems to be well now with this issue.
At the risk of maybe causing confusion, I'd like to use this thread to bring up another unrelated (I think) issue that I've noticed. It is similar to something I'd noticed previously with 1.1.7, but hadn't got around to reporting before 2.0 was announced, but now that 2.0 is out and the bug is there, I guess I'd better mention it. I was out caching today, looking for a cache I had previously DNFed. Because of my previous DNF log, the map symbol was a blue frownie. After successfully finding the cache, I logged my find and went back to the map expecting to see the symbol changed to a smiley. But not only was it still a frownie, but nearly ALL of the smileys on the map were now displayed as frownies. I tried refreshing the map, but it didn't change, and even if I panned the map to a completely different location and refreshed, most of the symbols that should be smileys were blue frownies. The only way to restore the display to normal seemed to be to force quit the app and restart; after that everything was back to normal.
I'd classify this as a non-critical bug, but I figured you'd want to know about it, if it has't already been reported many times. That's all; thanks for writing and maintaining an excellent app!