Whenever I have UWF (Unified Write Filter) enabled on Windows 10 IoT, the application that it needs to run will run way to slow. It takes like 30 full seconds for the application to open. This slowness isn't the case when UWF is disabled.
This is most likely due to failed writes, or the program expecting to find data but it wasnt there (restart /w uwf on clears everything) - i have experienced the same. Check the task manager and see if you can notice a lot of disk writes or CPU.
Check your file exclusions and debug which exclusion could be the culprit.