The answer back from R&D on this is that for DIAdem 8.1 you are limited to a maximum of 1000 User-defined (VAS-file) variables loaded into DIAdem memory at any given time.
You can spread your variables over a number of different VAS files and load and unload variables in batches to get around this limitation.
You can, alternatively, declare GPI-variables with the command OdsValAlloc()
Of course, if your variables do not need to persist past when the autosequence (script) ends, then remember that there is no limit to the number of VBScript variables available.
Regards,
Brad Turpin