Aaron it's interesting you bring up a potential software problem because right now I am trying to sort out a new PCV on a 2010 M8 that is having issues and it appears there could be a firmware issue. (power commander term for software in the PCV) It seems power commander might be the Microsoft of the after market tuning products and the PCV seems to require regular firmware up-dates, the latest firmware is V0.1.8.5, the brand new PCV I'm working with is running V0.1.4.0 and the tech at power commander says that's such an old version that I probably need to send the PCV in to them to have it up-dated. I have been spending a lot of time trying to get the firmware up-date off of Power Commander with no luck, I was able to up-date my PC software to the latest version, however I believe one needs Adobe Acrobat in order to download the firmware and that is an issue if one doesn't not already have it.
What we have found on the new PCV we have been trying to set-up on the 2010, is a lean condition and surging as well as no throttle....it seems to work fine above 5,000 RPM. This problem will not be there when one first starts the machine, we were even able to run around the field for about 10 minutes and set-up the autotune but then it starts (almost like it's a temp thing, like when the machine gets warm it starts acting up). The first thing we notice is throttle hesitation (lean), then the idle is fluctuating approx 4-500 RPM (2,200-2,700 RPM) at idle, then she won't take throttle at all. We've had this happen on 2 different PCV on this machine, with and without the autotune connected, fortunately the machine can operate without the PCV connected so we have just disconnected the PCV and ran the sled. We were trying to clean up the bottom end of this particular M8 at it was very rich coming downhill (always had been) etc and at the sametime lean due to reeds, air intake and can. When the PCV was working it worked well, however it's been a pain in the a$$.
We have even talked to the dealer about reflashing the 2010 ECU to the up-dated 2011 spec, the dealer gave it a try but to no avail, kind off pi$$e$ me off abit, Cat has had EFI for almost 20 years and they still can't seem to get mapping right. That's my rant, they didn't get my 09 HCR right either.
My long winded point here is maybe check your firmware numbers, you can do the by plugging in your PCV to your PC, click on "view"'(top left), click on ''device information" and you will see a firmware code in the list. Maybe there's a firmware issue that needs sorting out.