Normally after one flight after changing the call sign it gets lowercase. (I.e change the call sign, start a flight, then end the flight and change the call sign) After that it should be fixed.
There is a bug report on this: Callsign , Tail Number , and Flight Number gets capatilized - #3 by NeoKingRthur
Also-when seeking support from the community, make sure to post something in #self-service (Community Support) under the appropriate sub-category 