An update for anyone following this: 
 
The Annata support team have spent 28hrs and have:
	- Replicated the issue/bug (in our environment)
- Compared queries between the failed and successful scenarios but found no differences.
- Confirmed that WIP calculation and posting are handled by standard Microsoft logic.
- Debugged across ProjInvoiceId, ProjCostTrans, and AMCaseJournalPost_INT_Extension.
- Captured a trace recording for analysis.
Annata are continuing reviewing the code to determine if any Annata or customer-specific customizations are triggering additional WIP calculation or posting logic.
They are also investigating the impact of work order status on the ability to close work orders, and whether it influences WIP posting behaviour.
 
So in summary, no solution or answer yet, :-(   Fingers crossed for a solution from Annata soon that can be rolled out to all customers experiencing this issue.  
 
Additionally, Annata did finally confirm a number of customers had reported this issue, but all elected to investigate on their own as any support from Annata would be billable. 
 
 
Screenshot of email from Annata removed by a moderator as it contained an employee name from a person at Annata where it could not be verified if the person agreed to have this name visible on a public forum.
 
Kind regards
Phil.