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FTP File Corruption

I am FTP'ing from a UNIX server to a Windows Server 2003 using a batch script. The service has been running for years without incident. Last week I encountered a corrupted file. Data was transferred from two user processes on the UNIX server (tow separate processes, two separate files) to the Windows server using "put" and naming the target files (two separate files with differing filenames), but a small portion (about 300 characters) of one of the files being sent was recorded in both output files. According to my log, both transfers happened simutaneously. I was wondering if anyone has enough knowledge about FTP to know how this is possible. Do received files get recorded in a temporary work space before being given the final filename? I don't understand how part of the data could wind up in both result files. Thanks in advance for any input on this issue.
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