One of my Puma500's shut down on the gig a couple of weekends ago (at the very end of a very long, VERY loud night). It was also in the soft bag. It eventually came back on, but I'm sending it in anyway for a check-up.
My feeling is that as cool as that 'rack bag' is, it impedes the airflow enough that when you are really cranking the amp, it can overheat. I will not be using the rack bag any more.
There have been other posts through the years of guys having shut-off issues with the amp in the rack bag, and then never having another issue when they remove it from the bag.
My guess is, part of this issue is the massive low end that those heads reproduce (I assume due to the hi pass filtering being set much lower than most other heads). This eats up a lot of power and hence generates a lot more heat than heads like Markbass, Genz, etc, etc. The little GK MB2-500 also has this super deep voicing, and there have been quite a few posts of those hitting their 'safety shut-down' when really pushed.
I would suggest taking your amp out of the rack bag and using a nice Mooradian bag for carrying it around. They already have the measurements for the Puma... cost, about $125... super high quality, and the bonus is you will have a pocket big enough for two 3' speakons, a long, heavy duty power cable, and an extension cord.
K