Hi There,
I know I am responding to a very old issue. Even I had the same problem and wasted atleast 2days to resolve it and finally I found a solution which might help people in future..
Go to SMSY -> Product Systems -> choose the product-> SID-> change.
LMDB Browser will open up with and you should be able to see the last option from the Navigation Tree "Verification Check" click on it and run Execute Verification check(Synchronous) and you will see the status of few objects in RED and you can maintain(Action tab) click on +Maintain and select the missing product instance ONLY for your version and close after adding required products and SAVE.
Incase you don't know which product instances must be selected for your product then go through this link for more detailed info: http://wiki.sdn.sap.com/wiki/display/SMSETUP/Maintenance+of+Product+in+the+System+Landscape
Hope this helps.
Cheers