Hi,
It sounds like you went through the repackaging process with AS 9.5 SP3 bits, and opened the Repackager project, excluded some items, and then tried to build the ISM and MSI. And the excluded items were not really excluded.
Could you make sure to hit the Save button in Repackager IDE after making your exclusions and before trying to build the ISM and MSI? Due to a bug in Repackager IDE, sometimes it does not use the newly modified settings when you build if you didn't save first.
Please let me know if this helps.