What about the LM339?

There are a lot of voltages present on pins of the LM339 (or at least higher values (eg: 5.8 v 1.1)) in the problem board when compared to a known good one in the same machine. In the good board, there are 7 pins that have no voltage present, whereas only 1 pin of these on the problem board has no voltage, the others range from 0.4 to 5V.

Does this indicate the problem is th 339, or prior to the 339?