When troubleshooting, always isolate a specific module so you can focus on that. In this case, we want to understand if the signal coming into the VP-X is bad, or the flaps and trim are incorrectly configured on the Dynon. Let's focus on the VP-X.
Look at the position value as displayed on the VP-X Configurator. If these exhibit the same incorrect indications as the EFIS display, then the issue is in the position sensor wiring. The inputs for the trim and flap position sensor share the same power and ground circuits, so if there is incorrect wiring it may affect something that seems unrelated.
So, I'm about 95% certain your position sensor wiring on either the trim oro flaps is incorrect. Probably have two wires somewhere in the wrong pins.
Hope that helps.
RV-7 980 hours, IO-390, VP-X (sold)
RV-8 (flying a friend's)
Thinking about low and slow backcountry build.
VAF Advertiser - Aircraft Wiring Guide
Book to help with experimental aircraft wiring.