I think I have a similar issue, running a surface pro 4, just installed tabletpro2000beta42 and bought the whatever it was from the store page (which seemed to point me toward an older version of the installer for some reason? "tabletpcmouse1965")
I have an art pad ready made and saved out as a .ini file, I can preview it in the layout editor and it's the correct one, but I cannot for the life of me actually load it. I've gone to "Layout" and I see my .ini file there, but if I select it I'm still left with the default artpad buttons.
I don't really understand a lot of this, I'm not interested in the track-pad emulation stuff at all, I just like the look of your art-dock thing. I've fiddled with "full-screen" and other stuff but I'm still left with the default artpad docked to the left. Any ideas?