Is it just my game, or is the -15% for non-core CoT penalty gone? It's in the static_modifiers file, but if it's there, it's not showing up in the tooltips.
*edit*
Also I'd swear it looks like the Importation Act penalty is applying even though I never passed that law.
*edit2*
After playing a bit more, the penalties seem to have reappeared/disappeared to what should be their proper states. The main difference that comes to mind, I'd recently reached 0 Infamy when I checked before, and just finished a war where I gained 7 Infamy when I checked again.
You do not get the penalty in your owned CoTs.
Also, if you are in a Trade League and have less BB than your Trade Leader, you use his trading chances. That's why you might see the penalty sometimes, and other times not.