Yes, there is startup noise in the Mainline. This is a function of the 6C45 tubes themselves and the noises they make while warming up.
If you flip the amp off, then turn it back on somewhat quickly, you circumvent the warmup process and get a bit of a thud as the coupling caps recharge somewhat quickly. (The volume control position won't have any influence on this)
None of this is anything to be concerned about, it's all normal warmup behavior.