I know, i'm terrible at titles. :P
I just noticed that I won't get the various skill perks if I do as follows:
1 - I deploy any ship other than my flagship;
2 - I transfer command to a deployed ship;
3 - I deploy my flagship and transfer command back to her;
It happened using Uomoz's Corvus, but I guess it happens with vanilla too, here's a screenshot:
Spoiler
(http://imageshack.us/a/img4/9867/screenshot033gw.jpg)
In this case I should have 20% hard flux dissipation, flux speed boost up to 25% flux, flux speed boost +25su/s, but I have none of those. :)