I don't see any obvious signals or IC that might cause the problem.  If it were my radio I would remove the Logic board from its shielded enclosure and inspect the solder joints.  I have seen two older units from early 2006 that eventually failed intermittently (in 2015 I think).  When I inspected under a stereo inspection microscope (10-20X) with a ring light, using a micro-pick to apply pressure to each lead, I found about 40 joints that were pasty and would move under light pressure.  I could plug the Logic board into the Main, turn on the radio and get it to fail by slightly flexing the PCBA.

To repair, I had to clean the old flux off the joints first, apply new flux, then reflow each problem lead with a fine-tipped iron and just a little solder.   Normal hot air reflow wouldn't work.  After the rework the intermittent Logic board problem was fixed, although there were other problems in the UHF mixer circuit.  I didn't find any problems with the BGA IC's. 

Let us know what you finally find the problem to be and how you fixed it (hopefully).

Steve, W3AHL