What was you input into the MT? Digital or analog. The issue you had leaves me to believe you were running digital. If so make sure your pre is on and connected to you microtrack PRIOR to turning on the microtrack. If you need to reconfigure the recording settings on the MT (bit rate), then you must reboot the MT.
See my post in this thread:
http://taperssection.com/index.php?topic=118196.msg1621623#msg1621623and some user tips I compiled in the same thread:
1) make sure you have a decent external battery pack
2) reformat the card before a new recording session, but only after transferring your audio files of the MT and onto your computer, and after making a backup copy (dvd/cd etc)
3) make sure your preamp is on and feeding a spdif signal PRIOR to turning on your MT
4) if you need to change the bit rate on the device (from 16 to 24) then you should reboot the MT
5) use the HOLD button while recording, hit the volume button to turn on the backlight
6) have fun (most important)