NCI GCMS methane pre tune and PCI tune failing but NCI tune passing

We have a NCI GCMS 5977B. We are facing methane pre tune and PCI tune failing. It says, "Improper masses for mass axis calibration".
We installed EI source. Did auto tune and it passed.

After that, we cleaned CI source and installed back. Baked out for 12 hours, then tried methane pre tune, but its not completing.

Tried PCI tune, same error and its not completing.

Then tried NCI tune and its completing.

and we ran standard of MCCP, recovery is good. 

We tried with new CI filament, but same result. We tried with an EI filament also, but no change.

Please help to diagnose the issue.

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