A clean, brand new CPAP set up should not harbor any bugs to cause illnesses. Was your equipment used?
My theory is that it's one of two things:
1. You got a bug somewhere else and the timing is conincidental.
2. You are experiencing gas cramps from "aerophagia"--swallowing a lot of air with the CPAP machine. Some people have a lot of problems with this at the beginning. Do a search about aerophagia up at the top right hand corner to find descriptions of the problem and how to deal with it.
Better oxygenation from CPAP should bolster your immune system and keep you healthier in the long run.
Hope you feel better soon.
Phillips Respironics System One Auto A-flex and Humidifier
Encore Viewer 2.0 Software