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Even though MySQL is running and detectable, the node doesn't show up *and* the Register MySQL Server action *also* does not show up, so you are stuck. This doesn't always happen. This appears to be a race condition in the Database Explorer's logic for refreshing its nodes. The workaround is to restart NetBeans, and then it shows up.
*** Issue 128506 has been marked as a duplicate of this issue. ***
Making this a P2, as it seems to happen fairly commonly, and is a bad first impression. I'm pretty sure I know how to fix it...
http://hg.netbeans.org/main?cmd=changeset;node=aba1046202e0