It appears the issue is related to having MDA in use.
When an Account is assigned to an MDA Group, and Codes are assigned to the Group, each of the MDA Codes are added to the Journal during the GL Import, so if lots of accounts have MDA Codes assigned, each of the combinations are imported by the stored procedures, it is only when you run the update afterwards the MDA Codes not used for the transaction are deleted during posting.
When a large GL Journal is Imported and MDA is enabled, each Account assigned to the MDA Group is inserted into the DTA10100 and DTA10200 tables, so you can run into timeout issues as each of these records need to be processed.
To get around the issue I ran a script to update the MDA Analysis Type to "None" before the Import, then created a custom stored procedure to insert the MDA records and reset to the Type to "Optional", but broke these down to smaller imports, as you can still run into timeout issues.
Hopefully this discovery may assist others with similar issues.
Mick