I have noticed when playing ToA 1.96 that on gigantic maps about 3 years in or so some strange things happen after ending each turn.
After clicking end of turn everything is fine for the first say 30-45 seconds with the background music playing and the trun button greyed out. But then things get weird. I hear an initial "hitch" in the sound / music (at which time also maybe an events window or report window pops up or even a diploamcy screen from an AI or research completed screen). Then the audio gets very choppy (even looping / stuttering) and the game itself unresponsive / non-interactive to mouse clicks, etc. even though the turn button has come back. If I wait say another minute or so (with the sound /music all messed up and the game essentially locked) then finally the game seems to "catch up" and the music and animations play smoothly and the game is responsive and smooth again. Moreover all mouse or keyboard actions that were effectively queued up then immediately take place in rapid sequence.
I should mention that this only seems to happen on games with Masochistic or Obscene difficulty levels (haven't tried suicidal yet) where by this point in time the AIs have a lot of ships and fleets active.
Also note that I am using the trick of placing my cursor in an unexplored part of the map before I click end of turn so I don't have the horrid fleet movement drawing times I used to have (advice from Loupindour et al on these same forums).
I will follow-up with a reply post of a relevant debug.err for a typical game suffering from this behavior.
Sadly though I really enjoy ToA this makes the game unplayable for me in later game stages. Note that the problem also seems to get progressively worse as the game progresses ...