[Laffs]

Things that are different with the default hotbar and this one are:

1. The icon sizes
2. Background
3. Inclusion of name labels
4. The ability to show / hide hotkey numbers and labels

1-2 dont affect how the bars work
3 just a text box with show hide events linked to a button and the tooltip data that is sent down (basicly)
4 all this consists of is 2 buttons that toggle the visability of the numbers

Far as I know there is nothing that will affect how primary etc works off the window settings..

Have you tried to install the default hotbars and see if the same happens with them? I guess you would need to use them for a few sessions to give it a fair trial..