RE: channel folders syncing correctly
I've worked with this further and currently, channel folders seem to be syncing perfectly, so I don't know exactly what might have been the root of the problem.
In case it ever comes up again, here's what I know about what was happening.
After uninstalling awasu 2.1 and removing it's leftover folders, I did a fresh installation of 2.2. I then imported all of my existing channels from an exported OPML file I'd saved. None of the plugin-based feeds worked properly since I hadn't installed any plugins yet. That seemed normal enough. I did all subscriptions in rapid succession via the "quick subsubscribe" feature. I then organized a large number of channels into folders adjusted my program settings and uploaded a sync file to my ftp server.
Afterwards, I did a similar fresh installation on my other computer and synced from the FTP server. All existing folders except "my favorites" were deleted during the sync process and none of my new folders were added.
After using the software for awhile I began to notice that some of my other channels had been corrupted. For instance, i had channel for the "hack a day" RSS feed that instead showed the contents of one of my flickr photo streams. I noticed other channels that seemed to have somehow glued two feeds together.
So noting all of those problems, I uninstalled again, deleted everything, and reinstalled once more from scratch. (Still on the 2nd computer). I then re-added my channels from the OPML file a few at a time. Sorting each group into folders, making sure feed addresses were up to date, and that any broken plugin-based feeds were immediately deleted.
One I was done with all that organization, I saved a new sync file to my FTP server. Later i synchronized my home computer from that file again, and all settings, channels, and channel folders seemed to transfer 100% correctly. Once I was done on the home machine again, I saved a sync file to the server again and synced the work computer from it.
So far everything seems to be back to working as expected. Like I said, I don't know where the problem was introduced. Was it the rapid import from OPML? Was it a sync file? A bad original transfer to the FTP server? I have no idea.
But I figured that if anyone ever ran into something similar, or I encountered it again, this info would begin to help narrow down similarities and differences.
And since I haven't said yet.... Let me add that this new version is really nice. It seems to run more smoothly, The folders are great, offering exactly the functionality I was hoping for, including the ability to stick channels in multiple folders. The docking windows are also wonderful, allowing me to place everything where I want. I have run into instances where one window or another does not exhibit proper docking behavior, but it's difficult or impossible to replicate. And like I said, once their placed, the windows behave perfectly. Oh, and the search/indexing functions are also wonderful. I've played around with them and they seem both responsive and crash free.
Thanks for all your hard work. I definitely feel that paying the upgrade renewal was well worth it.