I've done a brief search, but haven't seen anything remotely akin to what we're seeing.
Users have enrolled devices (iMac and Macbooks of all varieties). Mostly Sierra still, but happening on both Sierra and High Sierra.
At regular intervals (seems to be dependent on the Check-in interval (in Jamf -> computer management -> check-in), all applications minimized seem to all pop back up. I myself haven't really noticed this behavior since I typically work across a few desktop spaces, but have seen this occur myself now that I'm paying attention to it.
Because it was tied to the check-in interval, I thought it may be tied to the inventory collection settings (specifically 'Collect Active Services' or 'Collect Application Usage Information'), but turning those off haven't made a difference. The endusers swear this only started to happen after we enrolled their devices.
Aye - that's kind-of what it was - took a while to recognize my recently pushed policy.
Specifically, there was a policy to add dock items in self-service. It didn't actually add items, just made the option to do so available. However, it did have recurring check-in turned on. Once that check-in was turned off (all the triggers turned off and 'make policy available in self service' turned on), we stopped experiencing it!
Thanks for the suggestion.