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ImageMate SDDR-92 & WinCE 5.0

I'm using a ImageMate CF card reader/writer with a Windows CE 5.0 system running on a Viper single board computer. On insertion of a CF card the light on the ImageMate blinks twice, then the CF card is recognised under WinCE as a USBDrive. Conversely when I remove the CF card the light goes out, and the USBDrive disappears from WinCE. I've written an application that periodically checks to see if a CF card is present, then tries to write a datafile to the CF card.
However... when my application is running on the Viper the behaviour of the ImageMate changes. Now the light on the ImageMate blinks 4 times when a CF card is inserted, and occaisionally removing the CF card does not register with WinCE. After that point WinCE thinks there isn't a USBDrive present, but the ImageMate light stays on, indicating that it thinks there is a CF card present. If I remove the ImageMate and use a USB flash memory stick instead then the application works fine, I can insert and remove the USB stick as many times as I like and the application writes data when it's there, and doesn't when it's not.
So, any ideas how I'm managing to confuse the ImageMate with WinCE? Is there a WinCE specific driver for the ImageMate?
Help! Iain