I was playing on PCSX 2. Controller was working fine. Went to chrome for a minute.Oooh - ya weird stuff like that happens sometimes.
And PCSX 2 wouldn't register the controller anymore until I reconnected it. Then it was fine while I was playing it.
I run into a lot of problems like that. Regardless of controller or emulator.
If I need to check on something, I usually use my phone to google something while I leave the game open lol.