Z endstop switch offset?

Ok so I'm hopeing this is an easy fix, I just need a little direction!

The Printer: Solidoodle Workbench

The Problem: When I start a print the bed goes through the auto level procedure and then raises the bed to push the z -axis endstop probe up so it can start printing. However sometimes it does not raise the bed enough to pop the endstop switch up completely and when it starts printing the nozzle is just a few mm to high off of the print bed this the filament comes out "wiggly". For the time being I've just been raising the bed manual after the auto level procedure in order to adjust for the difference and then the object prints just fine! But I obviously don't want to do that at the start of every print..

I'm pretty sure it has something to do with my my Z end stop switch which has warped just ever so slightly and has caused a minor "bow" effect on the plastic arm that holds the end stop switch which makes it to rest just a few MM higher then it normaly is. But then again I'm not positive, every 3-4 prints or so the problem doesn't occur.. So I thought I'd turn to the smart and helpful people on the soliforums for help!