We followed up on this one directly as it was logged via our support channel too, but I thought I would post the reply here for the benefit of anyone having the same problem:
Do your missing stored procedure names begin with fn_, sp_, xp_, dt_ or dm_? If so, this is due to a Document! X feature that prevents the Stored Procedures list getting clogged up with system stored procedures.
You can alter a registry entry to alter this behavior. Set the following registry value to cause Document! X to load all procedures:
HKEY_LOCAL_MACHINE\SOFTWARE\Innovasys\DocumentX5\LoadPrivateDBProcedures=”True”