So... I had more bugs last night and I fixed the last of them earlier today.
BTW, Steam internally stores a rank as '0' if it wasn't explicitly set. This is probably why the old wishlist system used to show you the last few items in random order every time you reloaded the page-- it sorted by rank, but then it got lost when all ranks were 0. This is probably going to happen on LT's as well, I don't know. I always give items a 'fake' rank if they're zero, need to see if it changes.
Now, I *think* I've found a bug in the new Steam wishlist...
Some items, for SOME reason, unknown to me, provide a duplicate rank. Due to this, the reworked sync tool would still drop some games and consider them removed. I had 13 of those. I fixed that to force unique ranks (basically I'm dropping duplicates to the end of the list), and I'm only getting 3 missing games now. (Not sure why-- but then again I don't remember those games either.)
It's okay enough for now... Please report your results.