I also own the McIntosh MA6900 integrated amplifier and my unit does not make a "popping noise" when I turn it on. I do not know why your unit is doing this. Please call the McIntosh retailer you bought the unit from and ask them.
Poping noise starting up Mcintosh MA 6900
When I turn on the amp using the standby button, I get a popping noise that is audible through the speakers. Not loud, but can be heard. The amp is just 1 week old. I had the MA 6500 in the same set-up and liked it so much I upgraded to the 6900. The 6500 made no noise, none. Is this inherent to the design (autoformers) or is there a problem? If anyone has the same experience or has suggestions, please respond, thanks.