atomz4peace,
I’m afraid we cannot replicate the problem with ME4S 8.6 on Windows 7 – 64 bit. Are there any associated error log entries? If so, please post them here (or attach the .log file).
How are you adding the Javadoc location? There are at least three ways into the jar’s property page.
Are you seeing any other strange behavior since you installed ME4S on your new system? One thing to note is that installing to C:\Program Files, may cause problems. Later releases of MyEclipse will not allow an installation to that location and defaults to different location, as detailed in this FAQ. If you’ve installed in Program Files, can you uninstall and re-install to a different location?
Other than that, some things you might try are to create a new workspace and import your projects from the old workspace. If that doesn’t work, try using the clean flag, as described in this FAQ. Lastly, a re-install may be needed, though I’d recommend the latest release (currently 9.1, but 10.0 is due very soon).
Please let us know if this helps.