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When a user sends a very large plot and reports data missing, or only a partial plot comes out, defrag the drive with the /TEMP or /TMP directories -- especially if the output file is then going to third party RIP software on a server.
Apparently, the process of spooling a file on the hard drive is sensitive to being contiguous. If there are too many fragments, the spooler seems to time out and quits sending the rest of the file, resulting in only a partial plot.