This isn't happening 100% of the time, but there are now 7 intercompany customer invoices which can't be completed as only one of two journals have been able to be posted against them.
Believe this is related to feature: Enhanced performance for source document accounting framework. And we can't disable it until we've resolved the problem with the 7 invoices which are now stuck.

There are 7 invoices which won't finish posting. Normally with these intercompany customer invoices, there are two journals posted for each. However, with these 7, only one journal was posted for each, the intercompany one has yet to be posted and is now stuck.

MS have suggested to change the number sequence, which didn't work:
1. created new number sequence
2. assigned to the Free tax invoice voucher
3. Press Generate accounting (and wait for batch job Accounting framework processor for journalisation with 1 parallel thread to finish). But same error still being reported in the error log: Error encountered while processing documents for journalisation process Document number: CGSA.INV001013 Voucher %1 is already used as at date %2.

Anyone experienced this problem and how to resolve? Any suggestions?