Tracey don't mess with my head like this, are you really seeing timewarping? Do you have the exact ships and missions? Why does nobody else experience it?
Until we were testing missions for AOTK2, I wasnt even aware of timewarping issues in EEK missions until DieHard pointed them out to me. Unless you are very familiar with the shiplist, AI ships that are out of era tend to go unnoticed. I have been seeing Heavy War Destroyers that should not be available in 2273 in mission.
I will start writing down the ships and missions for you.
Timewarping occurs as a product of using a particular ship creation method that works well in all other respects except the API "campaign year" parameter is broken, and therefore, it ignores YFA for ships. The telltale sign that this ship creation method is being used, is that AI ships created this way will have era specific drones. You will notice in the stock missions, and many of Dave's missions, that AI ships do not have era specific drones (but some do). All the EEK missions and now mine as well, create ships with era specific drones because they are using this particular ship creation method. I made a rather post some time ago outlining this.
This is not a new problem, in fact, its a very old one. I certainly don;t mean to alarm anyone by pointing this out. Will get you the specifics and we'll take it from there, in the meantime... relax, Bonk, its all good.
Personally, I prefer to have timewarping if it means we have no multiple host bug and we get AI removal in PvP. This is not the deal breaker that it may appear to be.