You could be using the wrong command for Power On. It should be the PS Key. Also, a manual change in the power state of the PS3 will cause the PRO's internal variable and the PS3 power state to get out of sync. You can either power cycle the PRO or manually power toggle the PS3. Using your remote for Power On or Power Off will avoid getting out of sync.
Alternately, you could upgrade to the PS3IR-1000 with the optional power sensing cable. That way you'll never get out of sync AND have the latest and greatest Schmartz product. Well, so far, at least...