Luis,
I can't test it with 6.1, but I suspect you're right about there being a change in the HTTP server behavior. In 7.1, anyway, it looks as if LabVIEW keeps track of open file refnums and throws an Internal Error 500 if a client asks the HTTP server for a file that is currently open in LabVIEW.
I don't know why the server would have to do this, and maybe there's some flag or configuration setting that could be tweaked to adjust that behavior. I'm not sure.
In general, though, I think ElSmitho's suggestion is the simple answer here. Can't you adjust your file I/O code so that you close the file between write operations? You said you couldn't close it, but unless you're writing data at a very high rate, opening and closing for each update shouldn't cause any real performance issues. If you do the I/O this way, you should find that the Web server doesn't throw the error anymore, or at least throws is very infrequently, when there happens to be a request during the very brief period when the VI is writing data.
Regards,
John