Tomcat server, save settings error on Gentoo

I'm trying to setup a tomcat server on my Gentoo box, however when it comes to save the settings IDEA generates an error.

"Cannot save settings"
"Cant find directory " The home and base directory do exist (and are different!!!). I'm confused as to if it is not saving because a directory in the config cannot be found (in which case why wouldn't it just tell me and save anyway?) or it cannot find the directory that it normally save things in (why would the whole program not explode then?). It would be really nice to know what that is trying to point to.

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