Hi James:
The runtimes are stored in the following location:
${workspace}/.metadata/.plugins/org.eclipse.core.runtime/.settings/org.eclipse.wst.server.core.prefs
On my local installation, if I start an empty workspace and add a runtime, that file gets created. If I restart, that file is checked for its content. If I shutdown eclipse and remove that file, and then restart eclipse, the runtimes are not found.
I would guess your first step would be to verify that file exists wherever your .metadata folder is stored, and that it still has valid content. Other than that, I'm not sure whether or not this would be cached locally or not. It seems to me that its not. As far as I know, all such settings for plugins are stored in the .metadata location.
Good luck, and let me know if you find anything helpful.