I very much doubt that this has anything directly to do with Winstep. But the issue certainly rings a bell or even two. Back when I first started using Windows 10 (only for a handful of specialist apps and one specialist hardware support, none of which were available for Linux back then - now only need the hardware support and 2-3 apps, and only occasionally) I experienced the 'moving desktop icons' syndrome myself. I fairly quickly discovered that the culprits were Virtual Multiple Desktop apps that I kept trying out, including Windows' own. (VDs were bog standard on Linux - almost? - from the start!)

A bit later a friend experienced the same issue, although he didn't run any VDs. On trial and error experimentation, it turned out to be down to a display management app - I don't remember which. It probably is down to some Windows bug reacting with a certain class of apps, and I suspect that the Winstep behaviour you observe is merely coincidental with this.

Just my 2 quid's worth.