Hello! Nice to hear that my suggestions worked!
About your last issue: are you sure that you configurated correctly the controller? Mednafen is a bit tricky. Read carefully:
When they say (for example) “GamePad#1:A(1)” you have to press the controller button that you want to assign. After you press, you will get: “GamePad#1:A(2)” (notice the 2). Here you have to press again the same controller button to confirm the choice.
After that, you will move to the configuration of the next button (B) , and this will continue after you will remap all the button that are related to the system you are emulating.
The rule is that you have to press two times for each button that you are mapping.
For example, if you are running a NES game, you will configure the NES buttons (A, B, select and start). If you are running a SNES game, you will configure the SNES buttons (A,B,X,Y,R,L, select and start).
Here you will get a bit more info:
Probably this sounds a bit complex, but really is very easy when you get it. The mapping method is the same in Linux.