We had this exact issue, it occurred roughly every 90 minutes or so-- at the same time Group Policy updated in the background. This occurred only over PCoIP for us, but try to replicate it by doing a gpupdate /force, your screens will flash if it's the same issue. For us this was caused by the "Configure PCoIP Image Quality Levels" ADMX setting, the issue was resolved after disabling that setting and allowing it to automatically dictate quality based on the bandwidth restrictions we set. In either case, if forcing a group policy update replicates the issue for you, it's likely one of your policies causing that like it did for us.
