The line in the config file you want to change is:
MapExtMem = 1
Change that to a 0 and see if it helps. You could also try using the WIP2 version of v0.6a (available on the SNEmulDS homepage) to see if that makes a difference.
On a side note, they do make Phat-sized 3in1s but you have to specifically look for them.
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