Lots of buffs with leveling errors in them. The two adaptive shield buffs, double front and backup, are both set as fixed level 0, instead of intrinsic. The levels are there on these abilities, but you can't access them.

 

You also have them set as ultimate abilities at the same time, I don't know what effect that has on them, if any. The standard Sins setup is that ultimate abilities are the one level, five experience level requirement ones, fixed level 0 abilities are for frigates and cruisers, and then the normal, intrinsic abilities are the multi-level capship abilities. You need two separate entities for the same ability shared between capital ships and frigates if you want it to level properly. You should be able to use the same buffs between them.

I think the fixed level change may be due to this comment

"removes a warning about some abilities being level Dependant"

Yeah, you can't put leveled abilities on a ship that doesn't gain levels.

Posted the fix in the onslaught bug report. The problem is the lack of experience requirements. You'll also need to change the ultimate ability tags or only the first level is accessible. Frigates and cruisers still get the first level of the ability even when using the Intrinsic value.