Gen, It sounds like the F1 actuator is out of center. The ACTUATOR is the mechanical assembly that engages the gear selected. First and second gear are on the same shaft with a common syncro, third-fourth, fifth-sixth, so I see why engagemnet from a different shaft to second would pose a problem and not first to second, the actuator is already in line for first-second engagement.The actuator has two potentiometer sensors to monitor shaft movement and if the movement is there but the gear does not engage it will default to neutral, also going into fifth gear is a default mode for missed engagement. I have seen this enough to put that first on the diagnostic hit list. They can test engagement with their SD3 tester, they should repeat the test several (a dozen or so) times to verify that the engagement centering is absolutely correct. There will also be Diagnostic trouble codes (DTC's) to correlate with the symptoms stored in the Trans control unit (TCU). The DTC's will read something like "opposite gear engagement", "gear engagement with wrong shifts" and or "gear release failed", any of these indicate the actuator being off center and needing adjustment.
If it were the clutch position sensor, the symptoms would be more erratic and not happen at the same time every time.Rarely do electrical problems repeat symptoms the exact way each time. If the sensor IS changed however, replace the clutch at the same time, especially under warranty,
you will save clutch labor charges, both are in the bellhousing. Hope this helps, best of luck.