While trying to invoke process model, I am seeing error in wm.prt.dispatch:handlePublishedInput. Error is [PRT.0101.9301] Error connecting to the ProcessAudit database for cross referencing IDs in the PE

I tested Process Audit and Process Engine jdbc pools and both are working fine.

does any one have idea what to check?

if you sure the DB connection is there, check if you have these tables in your PE DB:
WMPRTXREF
PRTUUIDPIDXREF

Could be storage or access issues with XREF tables in PE db!.