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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?

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I remember having this problem with older versions of KSP (around .16 or so?). Are you using the latest versions of KSP and mechjeb?

If both are up-to-date, I'd try installing KSP to a new directory (keep the original if you'd like). Reinstall mechjeb and try again. I've had a few cases where this has fixed odd issues.

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I haven't encountered this problem since I started bringing back the MechJeb module. The last time I updated I basically did a fresh install and copied over my save files, so maybe that solved the problem. – MBraedley Nov 20 '12 at 16:11

Make sure any sort of auto-pilot is disengaged. Sometimes that doesn't let you end the flight.

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