Sounds like the 7ender CS didn't cut that slot correctly in the first place. That E string must have been riding above the bottom of the slot, not fully seated in it (as in, the slot was not really wide enough for that string), otherwise, it too, would have been too low for the first fret.
The bass played amazingly well with the .105 E-string in there. No problems at all with seating or anything else. When the slot was too wide for the lower-tension .100, chaos ensued.