In multiplexing, you need to select one of the four groups first, before reading them because the same bits represent different values, this is what screws the emulators

1) Write a value to address 0xFF9202. This sets the
control lines on the multiplexers.
2) Read the values at 0xFF9200 and/or 0xFF9202. These
will have certain bits cleared (set to LOW) to
indicate which switches in a group are being pressed.
The value that you write in step one is made up as follows: it is a
long, whose lower four bits represent the control inputs of joypad A,
and whose next four bits (5-7) represent the control inputs of joypad
B. For example:-
0xFFFE Selects group 4, joypad A for reading
0xFFFD Selects group 3, joypad A
0xFFFB Selects group 2, joypad A
0xFFF7 Selects group 1, joypad A
0xFFEF Selects group 4, joypad B for reading
0xFFDF Selects group 3, joypad B
0xFFBF Selects group 2, joypad B
0XFF7F Selects group 1, joypad B
Once you have written the requisite mask to 0xFF9202, you can read
back the state of the joypad(s) from 0xFF9200 and 0xFF9202. Since the
joypad works on NEGATIVE LOGIC, a bit is CLEARED whenever a button is
pressed. In the table below, the first letter indicates the port that
is being read, so A FIRE B represents fire button B on the joypad
attached to port A. The exact bit that is cleared determines which
button has been pressed as follows:-
Okay, so having probably confused everyone now, here's the summary. To
read a joypad, simply write a value to 0xFF9202 with bit 0, 1, 2 or 3
low (and/or 4, 5, 6 or 7 for port B) depending on which group you want
to read. Next read from 0xFF9200 and/or 0xFF9202 to obtain a bitmask
giving the buttons in that group that were pressed, as in the table
above. Clear as Guinness or what!!?!?
This is taken from the following guide which is ESSENTIAL to better understanding the Jagpads...
http://www.gamesx.com/controldata/ejp_faq.htmThe guide URL abpve is really the only way its explained in great detail.. please read it

I hope i've been a little bit helpful lol, its a real nightmare, BUT, once you've written some jagpad code, mine above in the previous thread will make a LOT more sense lol