Ok guys, I have a success story to report!
Thanks to airline38 for his assistance - much of this is his information, although I've made it more verbose.
Here's my conclusion:
- As an antipiracy measure, the WiiU system update, at around 30-33%, unpacks the vWii iOS'es and checks them. Don't know if it hashes, checksums, or what.
- Bad check equals 162-0002.
- MISSING iOS'es equals "reinstall".
- Good check equals "ignore".
It seems to only check titles under 200. Anything higher, such as 236, 249-251... all irrelevant.
Presence of HBC, HBF, Config Loader, etc. ... all irrelevant.
It really truly ONLY CHECKSUMS THE SYSTEM iOS'es.
Now here's the kicker. If you touched any of them yourself? The checks are screwed. I don't know the mechanism - maybe it hashes them somewhere, maybe when you poke a title there's a flag set somewhere. I don't know! What I do know is that I used AnyTitleDeleter and REMOVED every iOS I had touched. That includes:
iOS36, iOS53, iOS56-58
Why had I touched those? Who knows. Maybe I ran brick...pimp...myWii. Maybe I accidentally installed the dumped WADs instead of using them as a base for 249-251 (pretty sure that's what happened actually). All I know is that they had been touched, and I deleted them, and that did the trick.
After I did that, the update ran FLAWLESSLY, replaced every one of them, and upgraded them!
I can also confirm that the WiiU system update DID update a number of the vWii system iOS'es. iOS59 went up from v8737 to v9249, for example.
Now, the real mystery - why do people who NEVER hacked their vWii have this issue? I can only speculate that it's possible for iOS'es to get corrupted somehow. Like I said, I simply don't know how this thing stores the hash information, or what specifically it is checking.
Here's one thing I've noticed which might be unrelated - the vWii has a somewhat elastic amount of storage. On a physical Wii, trying to install HBC without sufficient space would bomb out the process. On the vWii? It'll still install! Then you'll get "this Wii is out of memory" and the channel manager will pop up. I deleted "Lost Winds" which was 258 blocks, but only ended up with 239 blocks free. Is the vWii stealing memory from somewhere else? Is something getting corrupted by the channels which are too large? These are all questions I simply cannot answer - and this might be unrelated, but in my experience (admittedly 20 years ago) as a system level programmer, there is NO SUCH THING as "extra memory". SOMETHING gets stomped. I wonder if people who have this bug but have never modded their vWii did a system transfer from their old Wii and it was too big? Or maybe they had a few things installed already? I'm wondering if the vWii isn't simply prone to corruption, especially in the "gets installed by a game" iOS'es like 53 and 58?
Ok, enough rambling. I'm happy to provide more details, answer questions regarding what I did - I'll keep an eye on this thread for a few weeks, since you were all SUPER AMAZING in helping me out, especially airline38!