After diagnosing issue with SQL Profiler, determine a long query against PMPROJS table and then single record fetches to PMPROJT table. 

The behavour is intermittent as not all AP Batches are Project Job Cost entries so only occurs when particular projects are referenced in AP entry. 

Sage 300 PJC was not optimized to work with large open project data set, and does not filter by a particular project or phase, but queries the entire table to the record.

This issue has been brought to developments attention and product management is determining what resources may be required.