It's not a false positive. Your IMEI is 004999010640000 which is a generic IMEI deemed invalid by us in latest CM10 nightlies. If you restored from CM9 then it's also invalid on CM9. If you go back to CM9 and it doesn't pop up the warning, it's because the warning was not present in CM9, but you should go check your IMEI and see if it's still 004999010640000.
What makes that a bad IMEI? My phone works like a charm.
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