I noticed that my tunes from after June or July of this year would cause the OBD2 tests to never complete, specifically for the O2 sensor, catalyst, and other monitors. This causes the CEL/MIL to flash when you turn on the car (not the engine) and wait about 15-20 seconds. I'd run VCM Scanner, FORScan, or other diagnostic tools to check on the OBD2/emissions tests and they'd never complete. It's been about 10 days now with the current tune, and averaging 40-45 miles per day of mixed driving conditions. I looked and compared with my tunes from earlier this year and there's nothing I can see that would indicate I turned off anything. As it stands, the car wouldn't pass emissions inspection.

Any ideas? The ECU is a TC-1797 from a Fusion Sport 2.7 if that matters