I Just installed Mountain Lion and had the same problem I use FLashBuilder (which is 32bit) and MountainLion is 64bit, which means by default MacPorts installs everything as 64bit. The version of subclipse I use is 1.8 As i had already installed Subversion and JavaHLBindings I just ran this command:
sudo port upgrade --enforce-variants active +universal
This made mac ports go through everything already installed and also install the 32bit version.
I then restarted FlashBuilder and it no longer showed any JavaHL errors.