Hello Scubabiker03!
Question.... what industry are you in? Saying, is there an industry pattern or practice that would lead the internal auditor to believe end of month practice is not OK?
So if I understand, you have a procedure in place that specifies establishing an interval for each instrument enrolled into the system (e.g. six months). And in your procedure you also state that calibrations are due at end of month. So for an instrument calibrated in March and September, the calibration is past due on April 1. But the internal auditor is stating that won't muster on its own and requires some kind of justification?
Off-topic.... some of the most time consuming/ non-value added process activities I've seen implemented and abandoned not too long afterwards, were due to internal audit findings with no questioning, no citations, and a "just do it" approach.