I thought it wasn't happening anymore but after a bit of playing... Boffs skills reset to their defaults.
This happens to ground Boffs. Even to those without a secondary specialization.
Reproduction:
Train boff in any number of additional skills and select them as default. Play missions (switching from ground to space). After a time, the ground skills of the Away Team resets to their original ones.
Oddly, the Boffs retain their selected skills when logging out and back in.
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