Have you got Forceful pause screen checked?
With this checked/ticked I can replicate your issue - so might be worth trying that.
However I also have to have start up screen set up as below
If I tick Hide All windows not in exclusive full screen then emulator doesn't show - I haven't messed around with PPSSPP for ages so not sure what adjustments I may have made to it in the past to need it like this
Just for completeness have associated platforms set like this
Using PPSSPP 1.18.1 official release.
I do only have one screen though - so not sure if any of this will be of help
