Whenever I put a Power Commander on my bike, I also noticed it takes a couple cranks to fire the engine.
This was the case with my 2007 SV-650 and was the case with my 2008 WR-250R.
The FMF Power Programmer I now have on the WR-250R fires up right away.
Either way, no big deal.
I noticed quite a bit more performance and (very important) much better throttle response with the flapper eliminated, the AIS removed, the PC (or FMF programmer), full FMF exhaust system.
Much lower gearing is also important if you want acceleration. :)