So after it was suggested in chat, I decided to download and try the Mechanical Jeb plugin. During my trials so far with MechJeb, I've been setting up my staging such that the MechJeb module is discarded prior to re-entry. A strange thing happens when I disconnect this stage: it disappears. After that, everything seems normal, right through splash-down, until I try to end the flight. The confirmation dialog appears, but after that, it doesn't show the flight log, and it's as if I hit Resume Flight instead. I can't access anything other than the settings, and have to close KSP by way of Alt+F4. This of course means that the progress might not be saved, and when I re-open KSP, that mission can still be selected from the telemetry station.
Until I installed MechJeb, this never happened. Can I prevent this from happening by always keeping the MechJeb unit attached? Also, does having it active during the final staging have an effect?