Hello Catemae,
Yes this is most likely related to the medication.
While you can get a cold or flu at any time - before, during and after treatment - the start of treatment is often exactly as you describe.
What I tell my patients to expect is this:
You know that feeling you get just before you are about to get flu? Muscle aches, joint aches, headaches and feeling a bit miserable. That's what the start of treatment is often like and happens because you are killing off all the virus. It usually only lasts for a few days and responds to increased fluids, and simple analgesics like panadol (tylenol), aspirin, nurofen.
It should not last too long and will hopefully be better tomorrow that it was today.
As far as grumpy boss goes if you turn up looking sick and then say you have to go home it makes it very evident you're not having a sickie...