Hi Sam,
I just download all available update through the ASC and, as far as I tested it, seems to have solved that MIDI input configuration "save" issue!
I haven't time to tested it deeply, but it seems to me that the last update also fixed the M12 "skipping note" issue, at least for my DAW.
As far as the other V4 Collection plugin updates, they seems to work ok but I only experienced a strange issue with Analog Lab which, soon after the update, did not play any sound (even if my audio/midi card was correctly recognized and, for instance, midi input works), then after closing and opening again, it did play, and then again, after closing and opening, it did not; after that, it did play everytime I open it
Stefano