I do my upgrades and test them on my bench. There is only one engine on the TIU on the bench, and I have about a 25 foot run of wire between the TIU and the track. I also do my upgrades with pure DC on the TIU input channel. This is how MTH does them in their tech center. Note that when you're loading sound & chain files, you normally get a startup after the file loads, you can't stop that.
Once you've done a couple of power cycles after loading all the sound and chain files, they should not be coming up live with the application of power on the channel. I've done a lot of PS/3 upgrades, and I don't have this issue, so I suspect it's something in your environment.