The three most common reasons for these are as follows:

1.  During installation, the wiring for the magstripe reader may not have been connected to the main reader.  Please remove the main reader from the baseplate and connect the wire harness to the socket on the back. 
2.  By default, the magstripe reader is configured to read track 2.  It is possible that either the magstripe card wasn't encoded using track 2 or the reader was configured to read another track.

3.  The track on the magstripe card was not encoded using ISO encoding standards for that track. 

Please confirm with the customer on the magstripe encoding as well as confirm the configuration on the reader.