I'm haven't noticed any issues other than the not-centering. I haven't done any research, so I don't know what issues can be resolved with the analog deadzone.
@richiep I have the deadzone issue as well. I'm using the Ram controls USB adapter, and I think the deadzone is programmed in the controller. When I run a jstest on it, I can see the deadzone in the numbers, so I haven't gotten into the mame settings. I use advmame, so I'm not sure about the parameters in Mame4all, but there must be some.
Can you try advmame?
What is the USB adapter you're using? I was going to try to configure a Teensy.