Thanks for all the replies.
I've download the source files from winehq and compiled them. As a result, the problem has now gone away and the software works (I don't get any warnings now). People on the Internet claim to be using the Xilinx software with older versions of Wine, so I didn't think it was a Wine version problem. I can only guess the problem was to do with using a pre-packaged version of Wine (Debian Package). I had also tried other pre-packaged versions, all to no avail.
If everything had of worked as it should I wouldn't have been that bothered with the warnings. But as it failed, the warnings were the only clue I had to the problem.
Thanks again for the help.
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