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.
It would be worth looking into.