So far, the personal endeavours system seems to be working for me - objectives progress and complete OK, little boxes of goodies appear in my inventory - so far, so good.
Then I start spending the perk points, and oh dear.
I was trundling around in my Recluse carrier, which - what with bonuses and such - had around 120k hull and 20k shields.
Being the cowardly wretch I am, I wanted more protection - so the first two perk points I got, I spent on 1% bonuses to hull and shields.
And now my Recluse has 92k hull and 15k shields.
It's consistent with several other bonuses being missed out in the recalculations involved.... It's not much of a perk, though, is it?
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It seems to be fixed now, though. Back up to - well, a touch above what I'd considered usual (about 1% higher, in fact.) Maybe changing maps a few times, or relogging a couple of times, was all it took to bring the calculations up to date? Still, it was worrying while it lasted.