Is it possible the drive is old and starting to fail randomly? Have you tried running a disk checking program?
No, the extra graphics in BAT can be a burden on older computers and video cards, just like BlueMarble. Therefore we decided not to force it on everyone playing BUFFY. Sadly, due to how Civ modding works you can't use BAT with BUFFY in the same way you can use BlueMarble.
As far as non-HOF functionality is concerned, the current version of BAT = BUFFY + Graphics. I would expect BAT to run slower in the end game if your card isn't top of the line or at least very beefy. Both BUFFY and BAT integrate BULL which offers some nice interface enhancements over BUG alone.
That being said, BUFFY is quite old w.r.t. BUG and BULL features. BAT has been kept more up-to-date because there are no concerns regarding competitiveness month-to-month. We are working to get out new versions of all mods, but I don't know how soon BUFFY will be updated.
As for BUFFY and BAT, they are totally separate mods that ignore each other. You can install both, but when you play one the other is completely inactive. That will never change as it is how Civ4 handles mods.
BULL is dll changes. BUG is just xml and python. I know that doesn't actually mean very much to the lay user, but that is what it is.
Re late game speed - try using the BUG draw method for unit plots instead of vanilla or PLE - that significantly speeds up the game speed when using large stacks.
In my first game yesterday after installing BUG, I ran across an odd problem. I don't know if it's with BUG or a freak occurence with BTS itself. Every single unit in the game could be promoted all the way. My initial scout could get all possible promotions, and it was the same with every unit I produced. And every unit I came across too. All units had a pile of icons.
Maybe somebody want to look at it, in case it's a one-off, so I'll give a link to my save. I mention it in this post
It hasn't happened in the 3-4 games since, so I have no idea what may have caused it.
What I did (as you did) was give it a try to that "50
% speed DLL" that you mentioned earlier on.
Are you talking about CAR Mod--Civ Accelerated? Odd, I wonder if they cache the needed XP for the next promotion for each unit, and sometimes it's getting messed up.
The normal DLL uses a call to Python to get the next XP level, and I would bet that happens a lot during the game. It's probably a good candidate for speeding up the game by storing the number and only calling it again when the unit goes up a level. I don't know how often the AI calls the function, but I expect it happens at least every combat.