See issue 191300, if you repeat the same scenario for install as root / update as user, you will end up with enabled all updated features (even if you haven't used it before), which is wrong.
Used Full IDE.
*** Bug 191643 has been marked as a duplicate of this bug. ***
I guess the best fix would be to not update module that are not enabled.
*** Bug 119658 has been marked as a duplicate of this bug. ***
Integrated into 'main-golden', will be available in build *201012290001* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress)
User: Jaroslav Tulach <firstname.lastname@example.org>
Log: #191657: Offer only enabled modules for update