Do you have digital connections to the audio interface? If so, is your digital device clocking to your audio interface or is your audio interface clocking it? Anytime two digital devices are "talking to each other" one must be the master and the other the slave.

So for example, if you connect a digital mixer to the ADAT ins and outs of an 828, you might set the digital mixer to be the master clock and choose "ADAT lightpipe" as the clock source of the 828, in the FireWire control panel (OS 9) or MOTU Audio Setup (OS X and Windows). Or leave the 828 on internal clock and set the mixer to slave to lightipe or word clock coming from your interface. If you have many digital devices you can slave them in a clock "daisy chain" or make a word clock generator the master of all your digital devices.