Diplomacy adds stuff to Entrenchment. When you're playing Diplo, you still have all the Entrenchment stuff, like Starbases, mines, etc. You're not playing just one at a time, you're playing both.

This is a great game, nothing to feel upset about.

GOTY = vanilla Sins

Entrenchment = vanilla Sins + Entrenchment stuff

Diplomacy = vanilla Sins + Entrenchment + Diplomacy stuff

So just play Diplomacy.  Or start with vanilla and then work your way up to Diplomacy; it might be better that way.  Note that the pirates in Diplomacy are supposed to be very tough, in which case you may have to turn them off.