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Thanks again Zeus.
I've changed the drive letter to H, made sure my wrapper is using the same wineskin and wine engine versions, all mappings to $HOME are present and correct, but still no joy.
I've used winebrowser from the command line to open the FG data folder (H:\Library\Application Support\Fantasy Grounds) and that works so the mapped drive is configured correctly.
the problem seems to lie with winebrowser receiving both the path to the application folder and the data folder concatenated into a single sting, as in my post above. Not sure if this is possibly due to some compatibility issue with OSX 10.9.3 which is what I am running, as that is the only other thing I can think of.