I had this issue, mostly when switching between my clean sound (which is usually just analog chorus) and anything distorted.  I don't recall if I had this problem when I was using the M9's distortion, or more recently since I bought an OCD before the M9 as my main distortion sound.  I think for both. 

But anyway heres what I have running now and it works great somehow:

Guitar runs into the OCD.  OCD runs into the M9.  OCD's volume control is set to about 10 o'clock (pretty low).  First in the M9 is Vetta Comp, which is a great compressor and boost in my opinion (technically I dont think its supposed to boost, but it seems to, and with less ambient noise than the Boost comp).  I think I have the output level on that set somewhere between 80-100%.  Then after that I have the Analog chorus, with mix around 75%.  After that, whatever you'd like...I have usually analog flanger or dynamic delay.

I leave the Vetta comp on all the time.  So if I have chorus on, and then turn on the OCD, theres no volume difference, or vice versa.  Even if I am just playing super clean with just the Vetta comp on and I hit the chorus, also no large boost anymore.  I am not sure why it works, but it does. 

2 notes of this setup: One, some people will point out that distortion pedals are already performing like a compressor, they are right but having both doesn't seem to alter my sound.  I also get a nice sustain for soloing and dont seem to have any bad effects from also having it on when playing rhythm.  Two, others will point out that usually you'd prefer compressor before distortion and not other way around.  Ideally yes, and once I added the OCD to my chain I tried buying an additional external compressor/sustain pedal to place before the OCD.  It added a heck of a lot of buzz to the setup, which if you read up on compressors/sustainers is not surprising.  Somehow using the M9's compessor, in combination with the global noise gate for the scene, allows it to work better together and I can great great sustain without a lot of noise.  What also helps is that the OCD adds crazy boost, but since I have its volume down I dont get the hum you get when the OCD's volume is way up.  And don't forget that the key to this whole thing is that the Vetta comp always has to stay on.

Hopefully this helps you out.