This is so.... Embarrasing for Cryptic. It has almost been 2 months since the release of Season 4, and they still didnt fix most of our problems. Its no big deal. but Serious if its no big deal, I assume its no big deal to fix it either.
My values appear to be fixed for the time being, been ok for a few days. Only thing now (might be slightly off topic) but the Reman Covariant shield is supposed to be equivelant to a Cov Shield (x2 Cap) according to STOWiki. Mine was lower on my Defiant (Captain rank) and now its higher since using it in my Galaxy (Captain Rank) i've gone up a few levels but that shouldn't affect the base value of a shield that doesn't rank up with you.
If you know about this bug it's only annoying to unequip items so you can compare them with those in exchange, R&D or traders.
If you don't know about it you end up favor an equipped item with worse stats over a better unequipped one.