This morning I tried hooking up the rev2 Dexter board to my dragon's lair and noticed I was getting a spamfest of seek errors even without powering on the dragon's lair.
I hooked up my handy AVR dragon (hardware debugger) and noticed that sometimes the data from the ld-v1000 port would return 0xFF (expected) and sometimes it would randomly return 0xF7 (unexpected). This meant that pin A3 was sometimes 0 and sometimes 1 when it should always be 1. And since it was supposed to be using an internal pull-up resistor to force the value to 1 when unconnected, I concluded that something was pulling it down to GND.
Looking at the layout, I noticed that A3 passes through our NAND IC and concluded that this must be randomly pulling it to GND. Warren suggests that if I explicitly set one of the NAND inputs to 0 that it should fix the problem (I was not doing this).