When inspecting mechanical equipment we seldom find two identical devices running at the same temperature. Small variences are to be expected. But differences are a warning light to slow down and evaluate all the variables, which you seem to have done. The fact that the gearbox pulling less amps is the warmer one is a concern, but how much of a concern?
Several comments: IR is a great tool for finding thermal differences in a wide variety of mechanical equipment, but it many times cannot point to what is causing the problem. Vibration analysis and oil and grease testing and possibly airborne ultrasound are what may be called for in this case. If those technologies are not available then you should trend the two gear boxes against each other being sure to keep all variables in control. If the delta T increases between the two gear boxes you'll have significant proof that something in getting worse.
Rob
Rob Spring, P.E.
ASNT NDT LIII #65375
The Snell Group
rspring@thesnellgroup.com
800-636-9820