AS400 to IIS FTP slow transfers

[platinumblaze]

I use an AS400 application which needs to exchange xml files with a Win2K machine via FTP. Approx 20,000 files a day. When I start the application files take approx 2 seconds, as time goes by this starts to rise to 10-15 seconds. The FTP log in IIS shows a large delay in the reciept of a get command and the send of the file (the actual data transfer is less than 0.1s).
There is no excessive CPU or Memory usage. stopping and restarting the application on the AS400 (disconnects the FTP link and restarts it) brings the message speed back up.