Scrap the above seems the tables didnt empty when I did it.
Did it again and both old and new servers show 157 packages pulled from repository with joomla 2.5.11-5 offered.
What I did;
* rm -rf /usr/local/ispconfig/interface/web/sites/aps_meta_packages/*
* TRUNCATE "dbispconfig.aps_packages"
* resync packagelist from interface
Result = 157 packages offered
Tested on brand new box just built with no aps packagelist and same results - 157 packages, joomla 2.5.11-5 offered.
If there's a bugette in the ispconfig code I would suspect its not wiping "old" packages that are not being currently offered.