This topic seems to address exactly the problem I am experiencing, too. But I am wondering why this took so long to surface, considering the latest version has been released for 2 months now.
Anyway, this is my setup:
Recalbox 7.2.2 reloaded
Raspi 3 B+
64 GB SD card by SanDisk (class 10, rated for 80 MB/s read speed)
Original Power Supply (according to the PiHut) with 2.5 Amps
Genuine Sony Dualshock3 Controllers (2 of them acting the same) via Bluetooth
Games tried:
PSX:
Alien Resurrection (E)
Medal of Honor Underground (G)
SNES:
ALTTP Randomizer
The issue:
the controllers are not responing at all after a game is launched. Neither the ingame inputs worked, nor the hotkey commands (e.g., enter menu or exit game). Strangely enough, the controllers somehow worked at a time, but only some commands, which were all over the place (e.g., up = left). After properly configuring the controller in EmulationStation it ceased working ingame completely as described above.
Probably the solution:
This issue remained until I actually re-plugged my controllers and entered a game in that state. Now they work fine even wirelessly.
Another issue:
But in a few PSX-games I had previously configured for analog input (which Recalbox never saved) the controller is not detected by the game. Therefore, the games moan about the gamepad being unplugged. No setting I tried worked. But at least the EmulationStation inputs (Hotkey commands) still work.