Please never take my criticism as a lack of appreciation for you hard work and frequent improvements.
Sometimes tone really doesn't come across on the internet, but I've seen enough of your fussing to realize it isn't ungrateful fussing
As for not seeing any slowdown I'm actually very curious what folks consider to be non-slowdown, and what normal usage is really like. For me even on pretty good machines I see 50% or more slowdown (i.e. 300+ millisecond turns instead of 200ms) in relatively mild battles of 2000 ships kicking down the door into an AI system with roughly as many ships, etc. If you hit F3 during the game you'll get a variety of performance statistics including the lines "Last Process/Render MS" (sim time and render time for the last cycle, but changes really quick), "Last Turn Avg Process/Render MS" (average of last 4 cycles, iirc, somewhat more stable and useful), and "Last Turn Part/Full MS" (first number total of sim and render for last 4 cycles, second number is that plus any artificial delay to bring it up to 200ms, though I might not be reading it right).
And like Chris said we haven't seen your post in the bug forum; I'd have responded sooner otherwise.
Anyway, the changes I made _should_ not be affecting the rate at which units get their target lists, as I didn't really touch the throttling code or the "is this unit eligible for a new list" code, etc. I've certainly made changes in the past that caused a lot of problems there, and one point between 3.060 and 3.120 FRD was bordering on uselessness, but I made several changes to prioritize units in certain circumstances and ensure that every unit would eventually be "gotten around to" at some point, etc... and everyone was really happy with FRD and all that again. Currently there is a hard rule that a unit cannot get a target list if it got one within the last two game-seconds, and perhaps that is causing issues, though I get the impression from what you're saying that it's worse than that. Anyway, if you could make sure that your bug report is actually in the forum (and give me a link if I'm just being stone blind), and give a save if you've got one, I can take a look and see if anything untoward is going on.
Like I said, the changes shouldn't have been a problem for that, but I did do some pretty major refactoring of some fairly core logic (mostly collision checking, but also the actual computation of a target list, and movement code), so I'd be shocked if I didn't break *something* in that process. As-is the only reported bug that I've confirmed came from it was the Riot's ants-in-the-pants situation, which was pretty funny.
Anyway, thanks for the testing, hopefully we can get the targeting stuff ironed out. Actually, considering that this last batch of cpu improvements may well have increased sim performance by 30% in heavy battle situations, we may be able to use some of that in opening up the target-list throttles a bit more (or reducing that hard two-second delay, etc), but first I want to make sure I know what the actual bottleneck is for those ships. We've got the ants out, now to get the lead out