A lot of things it could be. When troubleshooting, you want to divide and conquer. You want to eliminate as many variables as possible so as to zero in on the problem.
1) Test your setup with an engine that is known to be good. If that engine runs with no trouble, then we know the problem is not the track.
2) Test your Berkshire using a different transformer. If it acts the same way regardless of which transformer you use, then we know the problem is not in the track, and not in the transformer, which leaves the engine.
3) Test your Berkshire without its tender. Remove the tender from the layout entirely - don't leave it sitting on a side track or anything. If the engine runs fine, then the problem must be in the tender. If it still runs poorly, then you can look closer at the engine to figure out why.
Re: the gears: On the 736, the gears are internal. There is a worm screw on the motor, which drives a worm gear mounted on one of the axles. The side rods transmit the rotation to the other the wheels.
This page has exploded diagrams for your engine (.pdf format), to help you get oriented. http://pictures.olsenstoy.com/736.htm
