I read that this happens when the valves are out of adjustment. When the engine heats up, the stems on the valves expands and gets longer. Therefore, the valves are't seating and sealing completely when the engine is hot and not making the compression necessary to start it (or easily start it).
Makes sense to me.
A guy on Totallyamaha said that he was having that problem with an Apex or RX1. He said that he wasn't getting the power that he was getting when it was new, wasn't hitting the RPMs and it was hard to start when hot. He checked the valves and the exhaust valves were out of spec. He adjusted them and said that it felt like he had gained 20 HP, he was hitting his RPMs and it started when hot.
I had three 2007 Phazers, two of them boosted. All 3 started like crap until the update was done. Ran much better after updated ECU too. Now this Yamaha Bulletin and recall was for cold starting but the new ECU helped mine start better both hot and cold. New ECU was just for the 2007 model Phazers
New updated ECU is 8gp-10 if yours says 8gp-00 you have the old one that had starting problems.