By you explanation I would suspect, Thermal problems, these are becoming more common as PCB density increases. Blow cold air over the devices and see if the signals improve (freezer spray is available to do this).
Knowing the exact devices would help, quite often devices are available in more thermaly efficient packages, this would also require thermal design considerations when doing the PCB layout. Initialy having a four layer board with 1oz power and ground layers would help both the quality of grounding and the thermal dissipation.
My first question on your design is why have you thermal relief on vias, it is not required and would imporove the ground copper pour. Also some of the vias look very close together with very little space. On these packages (quad flat packs) I would suggest using a decoupling capacitor that fits under the row of pins as this is dead area, plus you can reduce the decoupling loop.