This is an inherent problem with the design of wacomcpl.

Wacomcpl applies the settings as they are selected through the commandline utility xsetwacom and at the same time appends them to the $HOME/.wacomcplrc file which is executed as part of the X init process. When devices are added or removed at runtime, the wacomcplrc file does not get executed and the device settings stay at the default settings.

The proper solution to this would be to add a daemon that monitors device additions and removals but that's a rather tricky addition given the current code (and one more daemon to be aware of).

Development Management has reviewed and declined this request.  You may appeal
this decision by reopening this request.

As a workaround, the settings applied by wacomcpl can be re-applied manually to the device by running the $HOME/.wacomcplrc script.

On another note, I would like to point out that the configuration created by wacomcpl can be made permanent by moving the respective options into an InputDevice section or an fdi file.

for example, if wacomcplrc contains the line 
  xsetwacom set "Wacom Intuos4 6x9" Button1 "5"

This translates into
  Option "Button1" "5"
in the matching xorg.conf section

or into an fdi file like this

<?xml version="1.0" encoding="ISO-8859-1"?>
<deviceinfo version="0.2">
  <device>
    <match key="info.product" contains="Wacom Intuos4 6x9">
      <merge key="input.x11_options.Button1" type="string">5</merge>
    </match>
  </device>
</deviceinfo>