Hey Neilo, how's it going (apart from not too well game-wise based on your post)?
I haven't managed to get a game as far as turn 100 yet - I get to 60 or 70 then decide I could do better in the col rush, or need to try something different in the race setup - so not encountered any similar problems yet. The only time I am seeing any laggy effects is when the game is transitioning to or from strategic view - but it's a few seconds at worst. I've noticed that at the minimum strategic view zoom, some areas of the main view are still being rendered in full 3d - wondering if that could be an issue for an older card (I only run a 650TI myself). Wouldn't explain why it only happens at turn 100 though.
I'm playing immense or bigger, abundant everything, suicidal, all stock AI races, pirates off (as I read somewhere they were causing issues). Usually having 80-ish planets by the time I decide to try something different.
Core i7 920 o/c'd to 3.33Ghz, 12Gb RAM, 2Gb 650Ti, SSD (shouldn't matter unless your are excessively paging - unlikely).
There is definitely a main memory leak (or more accurately speaking a garbage cleanup) problem, as going back to main menu from a game in progress does not release any memory - but that shouldn't affect a game in progress with 16Gb RAM.
I am inclined to think there maybe a leak going on with GPU RAM that is contributing to this... do you transition between strategic / rendered views much? How much RAM does your 560Ti have? I have seen something very similar in another game, where GPU RAM was not being released between instances. You could try running a GPU monitoring tool (make sure it isn't overheating, confirm free memory etc) to eliminate that.
If I can focus enough to get to turn 100 and beyond, I'll let you know... but, well, new shinies to play with - you know how it is