2006 suzuki rmz-250 starting trouble.?

I have a 2006 suzuki rmz-250 im having some trouble getting it started. it starts fine when it is cold generally 1st or 2nd kick and once you have it hot it starts fine unless you let it set for more than 10 minutes then u almost have to drift start it. the bike was just rebuilt about 3 days ago! new top end,new clutch,new air filter,new oil change, new spark plug, carb cleaned, gas tank flushed, valves shimmed and checked and timing was set back perfectly. so i know its not a mechanical problem i think its an electrical problem what could cause this? my friend said cgi box but i dont know please help i need some advice from some experienced bike mechanics any help is greatly appreciated!