maybe...
what specific method were you using within GPP, and what settings were you applying?
when you 'disabled it', what did you actually do? did you unlink/delete the GPO, or, modify the GPO? if you modified the GPO, what did you change it to be?
it sounds like you may have been using GPP-Registry? and you were setting a key/value, and now, you've 'abandoned' that setting, possibly leaving it tattooed? (I am guessing, since there's not much detail above...)
if so, you may need to deploy a revised setting, either using the 'Delete' feature, or, perhaps (depends upon the setting you are using) a revised 'Update' setting..
Don [doesn't work for MSFT, and they're probably glad about that ;]