After this update I have been getting weird behavior when the game is under stress (like a shard chase...). Normally the game was running at a steady 100% pace or slow down to 80% or so, completely acceptable for endgame Fallen Spire gameplay (2 players, normal caps).
Now however weird behavior is happening. The game will run at 100% for a couple of frames (lowest performance profile so you can really see them), go down to ~70% for a couple, then up to ~130% for a couple, then back to 100%. This would then loop over and over again.
Slowdowns are fine and expected but the slow-fast-slow-fast got annoying very, very fast.
Do you have a save for reproducing this?
Incidentally, this may be related to multiplayer more than anything else, if one player's machine is a lot stronger than the other's. It may be related to the revised timing stuff. Basically playing "catch up" over the network. Slowing down the overall game speed with the minus key might help with that.
Basically, previously it may have been that both of your machines were chugging due to the graphics load combined with the CPU load. But now that the graphics load is effectively nil, the CPU is the factor, and during big fights that is a BIG factor. One way to test this would be for both of you to look at nothing -- basically empty space.
If you still see the slowdown and speedup behavior, then it definitely has nothing to do with the graphics at all -- those aren't being stressed in the slightest. In that case it's one machine running faster than the other in terms of the CPU and them having trouble averaging out the timing to keep it steady (which is a very hard problem to solve automatically without making EVERYTHING slower on average in that scenario).
Actually in older versions of AI War prior to Unity 3D, that used to happen. When that was the case, I'd just slow down the simulation speed during the slow parts and it would even itself out. Then I'd speed that back up again after it wasn't so overloaded for a bit. With Unity 3D, their internal code made it average that out for us pretty well, so that was less of a thing. But it also slowed everything down, all the time, to some extent. So that was kind of a bad tradeoff, actually.
What you're seeing now is probably the other side of that tradeoff, unless it only happens when one or both of you are looking at graphically intense stuff. But even then... frankly, it could be a mismatch in the GPU processing. Same sort of deal with the network timing. I'd say that using the plus and minus keys would be your best bet.
One other thing to test to make sure that this is absolutely network related (which means a syncing of time issue between the two machines based on one taking longer to do the same thing that the other one is doing) is to each take the game and run it solo (turning the other player off temporarily in that savegame), and then see if it runs in a jerky fashion or not.
If you are the host, I believe that you can see a little (WAIT) message pop up next to the other player's name repeatedly if they are the ones running slow. If you don't see that, odds are that you're the one running slow and that possibly they should be the host.
Boy, this really takes me back to the 3.x era.