I am making this ticket so that you guys were aware that I made this change - I have already done it in r306. Feel free to mark this as fixed.
AddOns should not call debugprofilestart() because this breaks the functionality of debugprofilestop() for everybody else (the timer gets reset). There is no reason to call debugprofilestart() because you can get the same effect with an initial call to debugprofilestop() that you subtract from the value from subsequent calls of debugprofilestop().
Also see http://wowprogramming.com/docs/api/debugprofilestart
It is impossible for your specific usage of debugprofilestop() to be broken by other addons that might call debugprofilestart() since WeakAuras does not call any external functions that may in turn call debugprofilestart() in the time that WeakAuras is interested in the value of the timer, but it is possible that your calling debugprofilestart() could break other addons, so I fixed it.