Just wanted to finish this off with a couple of quick notes. As Jasem said in another thread, Ekos uses the system time when a profile is started, not the KStars simulation time.

I got a fast USB SSD and set up to boot off that. No difference to my issue.

However, ensuring that the color overlays were off in KStars, selecting the "independent window" open for Ekos, and minimizing the KStars window seems to work around it.

Even with the color overlays turned off, if I do a "find" in KStars, though, the whole system slows to a crawl. What's weird is that using the "find" option in the mount control dialog, which brings up the same search box, apparently works just fine.

So I've got a functional workaround.