First, you run on very old firmware. I would strongly recommend to upgrade your firmware, maybe Bryston can help you on this. There was a link pointing to 1.75 firmware, but I can't find it...Or even upgrade for the new 2.14 firmware that is developed for BDP2. Then see if problem is there anymore
Second, you should do a health check for your usb drive; if it is as old as the firmware, maybe there are some issues there also
Maybe you can also clarify more: are this distortions random or each time for the same tracks? Also, the pops occurs in the silence between tracks of at the first seconds of a new track? I experienced distortions at beginning of new tracks in some particular conditions due to high processor usage, but not with CD quality, only with high resolution files.