Further update: Two other things have been changed that would affect a VA profile.
One is an easy fix, much like the one mentioned for the side panels. They've added an extra prompt on the Systems tab, so you don't just click on a module now to toggle it, you have to click on it, then choose. Not sure what the intention of adding that extra step is, maybe future things, but for now, just adding another key press for the selection should work.
The other is a bigger problem. I haven't looked at the update today, but didn't see it mentioned. When looking at Contacts the station for a long time has always been the first one on the list, making it easy to use a script to select that one for the request docking prompt. So far in beta, any players within range will pop up first on the list, and of course there's no way to tell VA the difference, so this breaks that functionality. I've reported it already, seen others do the same, so let's hope that they'll revert back and maybe it's just the side effect of something else and not on purpose. I made a point in my report that a lot of people are now using the voice packs, and breaking things like this won't go over well...especially when one of the was done with the help of one of their own (Verity).
Keeping an eye on others as things progress.