The Jrk's acceleration limit parameter only limits the increase of motor speed, not its decrease. The "Motor Options" section of the user's guide says:
Max. acceleration limits the amount that the duty cycle can change by in a single PID period. For example, if there is an acceleration limit of 10 in both directions, and the current duty cycle is 300, then the duty cycle in the next PID period is limited to be within -10 to 310.[/quote]
So even with your acceleration limit of 1, the jrk can go from a duty cycle of say 400 (out of 600) to a duty cycle of -1 on the next PID period, -2 on the next period, -3 on the next period and so on. This means that the jrk will be driving the motor in a direction that opposes its inertia. The stall current of the motor is 5A and your power supply only provides 3.33A so this could break the fuse.
To avoid this problem, try setting the "Brake Duration" parameter to something non-zero. Then, instead of going from 400 to -1, the jrk will operate at a duty cycle of zero (actively braking the motor on the jrk 21v3) for the amount of time specified in the brake duration parameter before it switches directions. While the duty cycle is zero, the motor will slow down due to the braking, but it can not draw any current from the power supply.
Regarding your input: If the output voltage on your pot doesn't change in the ranges 0-100 degrees and 200-300 degrees, then there is nothing the we can do to fix it, but it seems unlikely that the pot would be designed that way. Have you looked at a graph that shows Input, Target, and Duty cycle while your turn the pot through its full range of motion? What are your input scaling settings? To get the input working nicely in your system, you should change the Input Scaling parameters so that the max input value (~4095, 5V) gets scaled to a target of 2648 (duty cycle +600, full forward), while the min input value (~0, 0V) gets scaled to a target of 1448 (duty cycle -600, full reverse).