Heres a quick overview of the button presses:
Starts off raised.
Press once - should be sunken but stays raised
press again - stays raised but it should be at this point
press again - the button goes sunken
and from here on in the button acts like i want it to, its just the
first time i use it.

Here's the code im using if anyone can help me:

    if {$phaseInverterActive == "true"} {
        set phaseInverterActive "false"
        .phaseInverterButton conf -relief raised
    } else {
        set phaseInverterActive "true"
        .phaseInverterButton conf -relief sunken
    }

checkbutton .c1 -indicatoron 0 -text "My Button"
pack .c1