Thanks for the suggestion iojam, I was already in the data dir when checking the compression with zcat.
I've done some more digging and its definitely something to do with the gzip compression turning that off in the config fixes the issue. We've not had any issues with standard gzip support on the forums, but something in the sitemap code seems to be triggering an issue with it.
After looking at the code which is only a few lines I can only conclude the issue is with the underlying php function. There are a number of bugs still open in php's bug tracker which may be the cause.
For the time being we will live with gzip off.
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