I believe I've found my issue, because I have two different signals to capture when testing one single vs both together was causing my issue. If I look at the expanded function within the Capture bean this is what I see:
Cap1_GetCaptureValue(&Sig1Time) is expanded as (((*(word*)(&Sig1Time) = _TPMC0V.Word), \ (*(word*)(&Sig1Time) -= Cap1_CntrState)), \ 0U)
Cap1_Reset() is expanded (Cap1_CntrState = _TPMCNT.Word , (byte)0U)
Cap2_GetCaptureValue(&Sig2Time) is expanded (((*(word*)(&Sig2Time) = _TPMC1V.Word), \ (*(word*)(&Sig2Time) -= Cap2_CntrState)), \ 0U)
Cap2_Reset() is expanded (Cap2_CntrState = _TPMCNT.Word , (byte)0U)
but when i have only one bean enabled this changes to:
Capx_GetCaptureValue(&SigxTime) is expanded (*(word*)(&SigxTime) = _TPMCxV.Word , (byte)0U)
Capx_Reset() is expanded (TPMCNTH = 0U , (byte)ERR_OK)
Because I read TPMCNT as part of a system tick too, the single enabled bean version where reset is setting TPMCNTH = 0 seems to be the source of this.
Thanks again, D