As far as lights switching on/off between changes, I don't get what you mean.
Let's say that your master/slave mode operates off being "sound activated". The only light listening is going to be the master. The slaves will listen to the master's signal.
This is a lesson I learned the hard way and confirmed it on the forums. I will get specific because it helps.
I bought a pair of Color Fusions. These must be manually addressed using DIP switches, including their mode. When making changes like this, you have two choices: DO it with the fixture not receiving power, or if done while the fixture is ON, then power cycle it after changes are complete because the changes aren't "live".
If you're changing the lights from master/slave mode to DMX mode, or doing a pan or tilt invert, I think it may be normal for the light to switch off and back on briefly as it resets itself to the proper mode. With my Chauvet Q-Spot 150's, I regularly use the pan invert on BOTH fixtures. I think this is because I am confusing what the FRONT is of the fixture, but Chauvet won't answer me that question. At any rate, when I do the pan invert, the light "resets" itself after I enter that value in via the panel menu system. To me, this would be normal. While the fixture has I think 540 degrees of rotation via DMX, the light clearly has more rotation capability. I think this is to compensate for being able to do this inversion. I think the light COULD technically rotate a full 720 degrees of rotation(twice around), so this leaves an additional 90 degrees of "wiggle room" on either side of that 540 usable degrees, hence able to fully support the pan inversion.
It's almost like you tell the light "this is how you have to behave now" and then it seems like it "reboots" itself to behave properly.
If the lights are switching off and on in response to instructions from the master fixture, that would NOT be normal.
Also, typical warning stuff: Use DMX cables, not microphone cabling. I am not sure if a DMX terminator is necessary in a master/slave mode even when used for long runs. I know that DMX cabling and microphone cabling looks and from a pin to pin pespective is totally interchangable, but they aren't. DMX cable is data grade at 120 ohms, while microphone cable is typically rated at 600 to 1000 ohms. While XLR microphone cable WILL work, it's not your best option. If it comes down to a cost issue, let me say that for the most part, DMX cable is going to be priced at or below most microphone cabling of the same length. Unless it's crappy XLR cabling, in which case the DMX cabling would be more expensive.
I ran my lights using XLR for years. Worked GOOD. Changed to DMX cabling, works a LOT better.