This has started with the current puzzles ie 2259. 1) If I am running 2 clients and I try to flip from client A to client B I have to do it several times before the change occurs. 2) I am often finding that the client that is not on current display on the screen has stopped instead of continuing to run on it's own. This has never happened before.
For comment (2) on a Windows machine, find the directory where log.txt and scriptlog.default.xml are stored. I often have clients that are "not responding" or slow to update what they are displaying. Sometimes I even have clients where the gui has disappeared completely. Despite these things, I can see that these clients are still running because their log.txt and scriptlog.default.xml files keep being updated. I keep such clients minimized as much as I can and monitor their progress using their scriptlog.default.xml files.
Also, at some point in the recent past, I could run 4 Foldit clients at once on my best laptop. These days just running 2 Foldit clients makes this laptop seem very slow. I've also found that disabling the Objectives lets recipes run much faster. I think that some Objectives (like BUNS) that make the score jump or fall quite abruptly also make tools like wiggle take much longer to settle. It isn't just the time cost of calculating the Objective. It is how the wiggle tool behaves when the score function makes such abrupt changes.
Also for comment (2) on a Windows machine, each Foldit client has its own entry in the Task Manager. In the Task Manager, you can set the Priority and Affinity for each Foldit client separately. The Priority tells how far in the background to put each client (Above Normal, Normal, Below Normal, and Low), so Above Normal clients go faster than Normal clients, and Below Normal clients go faster than Low clients. Perhaps one of your clients seems to stop because it is a lower Priority than your other client.
Affinity tells the computer which CPU(s) to run each client on. My best laptop has 4 CPU's. I usually assign each client to a different CPU using the Affinity setting.
There are some foldit functions which may freeze a client.
For example use a puzzle with a lot of locked segments, and run Acid Tweeker. You may realize after a while a frozen client.
You may also try to change the loop into helix using foldit functions and vice-versa in a loop to create a freeze event. The presence of locked segments may "help".