Make sure you set DPI setting in IDKit SDK correctly before performing template extraction. IDKit SDK is optimized for 500dpi and images in different DPI are internally converted according to the DPI setting you specify. Setting accurate DPI is essential for matching fingerprints from different sensors.
In general, error rate (false reject rate) is higher when matching fingerprints from two sensor types. The increase in error rate is caused by distortion of fingerprint images by sensor hardware and firmware. Scanners using different technologies tend to distort fingerprints in different ways which makes them look less similar to the matching algorithm. You can adjust matching threshold to control the error rate to some degree.