I too have a very similar problem. This is the behaviour I see:
Choosing path through the file picker dialog, with a path like this:
…leaves the input field with the path empty, so I can not add it
Typing a relative path into the input field also does not work, then I get the error message mentioned in the post above.
The only thing that works is typing in the absolute path to the ressource. This is really annyoing…
I also have another problem which is related, I think: when I want to create a new certificate for a release build and use the file picker to choose the destination, Flash Builder crashes right after selecting the location. Every time.
Please let us know how this can be fixed!