Same for me, on pc windows Store version. Arrived at FL290 as requested by ATC, altimeter on standard and keep saying I am 400ft below assigned altitude.
Seems that ATC still keeps the ground QNH for any flight level, even above transition altitude.
Should be great also to have ATC to detect local transition altitude or at least the one input in the FMS to change to standard. can be more realistic and seems be simple to have an if/else on the transition altitude vars.
By the way, hope to have a quick fix for the standard QNH as fast as the previous fix. It is almost perfect.