I generally book through a TA, so can't speak directly to your pre-populating problem. But as concerns OLCI, I'm finding the opposite--the website is becoming more functional over time.
I assume my TA always enters my passport details on each booking. But it used to always be that the system would "lose" that information by the time OLCI rolled around, necessitating re-entry. Lately, everything except the passport expiration date shows up pre-populated in OLCI.
Do you re-enter the information for each itinerary in MMB after you book? While it's a pain to have to do it when they should already have your info on-hand, I wonder if that would at least smooth your OLCI (especially if you're checking in from a smartphone on the road).