Hold on, i'll make it more clear
This is what I think is happening according to all the ways I've tried to figure it out (which is a lot)
The R4 (and action replay cart) is programmed to find the mastercode:
Code:
C0000000 023DF000
F20081CC E12FFF1E
However, on the action replay cart you can specify your own mastercode (M). Not so on R4.
That is why AC:WW doesn't work, because it's mastercode is different
However, YGO:WC07 does work
I hope you understand what I'm trying to say
If you need info about mastercodes, read cracker's trainer guide
http://gbatemp.net/index.php?showtopic=44410&hl=