I took an IC job with a national and haven't really ever worked as an IC before. - IC Question

Basically, it's been working out fine until one day last week when I received an email from the transcription manager saying that was "short on my time" on one specific day.  I was confused because while I agreed to work first shift on specific days, I wasn't aware that I was strictly held to a specific schedule and wondered how they were keeping track of my hours worked because I do not punch a time clock.  I assume they are keeping track of the hours I'm logged onto the system, but doesn't seem to gel with the concept of being an IC. 

I always send an email whenever I have to be away from my desk for an extended period of time (i.e. longer than an average lunch break) and even when I am taking a lunch I send out an email or make sure it is noted on my IM status.  So now to feel like I am having to answer for some sort of phantom missing time is kind of irritating me.  I haven't said anything about it to anyone.  Just simply said "hmmmm" when I was told and then listened to her spiel.  I didn't offer an explanation because quite frankly I felt didn't really owe them an explanation, I couldn't really remember specifically what the explanation may have been, and finally, as I said above, I always send out an email or IM and so I assume that is exactly what I did when I was away.

So am I right to be a little irritated?  I like the job so far, but I just left a job where the MTs were held under the thumb of the supervisor and I had to document every trip to the bathroom and I assumed as an IC, I would not have to go through all that nonsense anymore.