Will, my experiences are somewhat similar with yours, and if there's any "pattern" to them, this is what I've noticed, tracing things back from the random erroneously posted elite bonuses for LH non-transat flights.

These bonuses only have appeared when the carrier entry on my MP summary show L#. In every one of these cases, I was booked on a UA ticket with the UA (codeshare) flight number. Interestingly enough, in every situation, this only ocurred when I checked in in Europe with LH agents (in stations other than FRA or MUC). And thinking back... each one of those check-ins took a long time and required the check-in agent to seek assistance...

So I don't know if this is a systems issue, a station issue, or an agent issue... How was your check-in experience at JNB?

Now as for expediting your future check-ins at LHR, assuming this is not strictly an agent issue, I would guess that having the ticket issued with the LH rather than UA flight numbers would make things go more swiftly.