As far as I can see, the EB Jr is a volume pedal, not an expression pedal. This means that it will have a logarithmic (non-linear) characteristic, which would explain your 50% problem, and also has a very high resistance (250k) which would explain the 100 problem.
Essentially, the 'Factor wants to see a linear pot with a resistance of about 25k. A true expression pedal will have this (some have adjustment), or, if you paricularly love the EB, some people change the pots for expression pedal use.
