Nothing unusual about this. The Flextone III has two 75 watt amps, but only one of them is connected to it's built in speaker. When you add the extension cab you're enabling the second amp and doubling its output. It's freaking loud! Check out the ping pong delay to start with. It's pretty cool. I have an M13 effects unit that offers a ton of stereo effects, (Chorus, panner, delays etc.), and you have the patience to connect your effects using the stereo effects loop, using the 4 cable method, you can get some absolutely mind blowing sounds out of this rig. If you have an FBV foot controller your options for witching tones and effects are limitless. It's a great rig.
* actually, just read your post again and sounds like you're not new to this rig and that your issues aren't just an overall increase in volume. I would backup all of your settings via midi, do a factory rest and then as you suggested, try reloading the tones to see if that resolves the issue.