It looks like it might be a partially coded section. The actual line in modifiers.txt for the ballpit is this:
Having a Ball! Muscle Percent: [pref(ballpitBonus)], Mysticality Percent: [pref(ballpitBonus)], Moxie Percent: [pref(ballpitBonus)]
Basically, it's reading your personal preferences for ballpitBonus. If you have 350 balls in the pit, set your ballpitBonus to 35 and all should detect modifier properly from there on.
The issue is that your preference doesn't appear to correctly be updating currently though, at least not for you... Appears that it's supposed to automatically update, based on consequences.txt, but the default if the autodetection fails is 1% (found in defaults.txt).
Basically, someone needs to troubleshoot consequences to make it actually work properly for detecting percentage.