It is possible to post between sub ledgers in either of two ways:
A VAT Journal will use the default Vat Control and Bank Account codes rather than those of the Sub Ledger selected, so unless these are changed at the point of posting, the lines will update across sub ledgers.
Analysis codes also take the default control account and so if they are created via the Nominal account screen this will need to be updated manually.
Both of the above are logged as issues with the development team and will be resolved in a forthcoming release.
To resolve this issue Support will need to run some scripts on the database. Therefore please raise a new case online and reference the title of this article and please include details of the transactions affected.