The AFE intake probably stretches the intake a little tiny bit and opens up the crack in the intake boot. Search for a DIY in the intake boot. It's pretty common for it to fail.
I have a 325, which I understand isn't who you're asking for responses from - I read

– but this slight physical stretch seems to be true in my case (for 325s) and for 330s, because of the differential angle of the MAF when connected to the AFE intake vs. when connected to the stock airbox. I did get SES codes after installing the AFE (the same ones you got, bank 1 and 2), but after adjusting the intake (shifting it as far as possible so the differential angle was as small as possible) and clearing the codes, the codes have not reappeared.
I definitely did not alter/knock the MAF while installing. If I did, then I would be having this same problem with the OEM airbox installed.
Another thing to note is the inconsistency of the comp in relaying codes and also the time/mileage required for the comp to reevaluate after resetting. For example, when I originally got the codes with my AFE, I removed it (this is before I reinstalled/readjusted it), cleared the codes, and put my stock airbox back in, because I needed to pass my emmissions test that week. When I got to the test center and they hooked up to the OBD2 port, they ran the diagnostics and said that I had driven long/far enough for the comp to reevaluate after I reset codes.
Just my 2 cents, don't know if that helps.