I was told that the CM build don't necessarily get along with apps2sd. If you have the Cyan Recovery I was told to do the "Fix filesystems" option after applying the update. I tried that twice, the first time (while still in recovery) it said that it failed, the second time it said that it worked. After that everything was working great!
sorry my bad, i was using the app to actually create the fat32 and ext2 partitions
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