>> All the clocks (pixel, line, and frame) are active
My display also had a DBEN signal that was driven from the BIAS signal of the PXA. I think it is used to gate the clocks to the display. If DBEN is in the wrong state, the display won't clock in any data.
>> To see if the panel still works, I tried an experimient. I manually connected the LDD0 to the +3v supply, expecting that it would change something on the screen. clocks (pixel, line, and frame) are active
Did something change?
I have a little pcb that fans out the hirose connector of the display into a ribbon cable. The vdd trace on the little pcb actually went of the board, so the display was getting no vdd power. So the display was totally black. Have you checked the display is actually getting voltage?
So, you see the right clock frequency on the scope? What frequency? What levels are you seeing? What does the display spec for required input levels?