Personally, I would add the path locations into the default profile for all disciplines and build the grouping so all disciplines can essentially access all of the palette groups. I would then setup default workspaces that would switch the tool palette groups as required.
To answer your main question - the display order is controlled by the user's AWS file. The AWS file keeps track of display order for the loaded palettes (tabs), the palette content (tool), plus the available palette groups. When you switch out a palette group it simply adds the new information to the bottom of the list - you would see the same issue if you added a new tool to a palette and simply moved it up in order on the machine it was added on. If it was a netwrok push the new tool would be displayed on your machine in the correct order, elsewhere it would be located at the bottom the the tool palette.
You really have two options: live with the order change and ask your users to move them up in order or try to replace the AWS file out.
The reason I say to pull in all of the palettes is because it is easier to deal with the AWS file if all of the groups are available. The biggest issue with swapping the AWS file out is this can only be done by switching to a new profile or copying the file over when AutoCAD is closed. I would make the switch in AutoCAD by moving over to a temporary profile and copying a network saved copy of the AWS file that was created on my local machine. I do it this way because I'm able to capture the name of the user's profile name to both switch in and out of and locate the AWS file to copy over.
If you look at the following link you can see a custom routine I use to accomplish the AWS swap: Tool Palette AWS
As I mention in that thread, our setup is highly customized but this will allow you to do the basic swap.
Rob