Well from what you have said it's hard to really diagnose the problem.
I know it was working before I connected it into the mod
It would have been best to pull the battery from your mod and hook only
it to the charger, that would be the test to see if "it was working before I connected it
into the mod", in other words you really don't know that it will in fact charge
your battery correctly (cuts off at 4.2V etc). It seems like it should, you assume it will... but without the simple battery only test it is an unverified assumption. You now have
2 potential areas that need troubleshooting. Does it charge the 18650 properly? Is there a problem with your mod wiring?
Did you do the full gamut of continuity checks, checking for any shorts, before plugging in the charger? I assume you were very careful with polarity.
Maybe someone who has actually used the eGo charger for standard batts will chime in.
In my early days I used this KR808D-1 universal charger with 14500's and 18650's, it worked fine charging the batteries to about 4.15V, but the 18650's took a long, long time to charge.
This MadVapes one works as many have used it internally.
MadVapes e-Cig 'How To' Tutorials ic - Added a USB Charger to a 3.7V Box Mod