Sorry to be pushing this old thread. Since I continue to run into this problem, I have an additional question regarding this one:
I have a Recalbox 4.1 setup that suffers from the problem and on an alternative SD card I'm running 4.0.2 which did - indeed - fix it.
On the 4.1 setup I did change the global resolution for ES to 720p as well, so technically there's no longer a resolution switch happening between choosing a ROM in ES and Retroarch running it. The problem remains though and I wonder why this is ?
Interestingly running ES in 1080p and changing the emulators to run in 1080p as well fixes this for most users. Why doesn't the 720p/720p combo achieve the same ? Unfortunately the Pi3 isn't powerful enough to run the emus in 1080p when using various shaders, so 720p is really the best option.
Any insight is highly appreciated - thank you guys!