Many of the "burn bootloader" instructions won't work on a MEGA2560. Optiboot doesn't work on it, for instance, and neither does Arduino as ISP. You should start another thread, and describe "acting very strange" in a lot more detail. From your description, it doesn't sound like a bootloader problem. The bootloader is ONLY used to load new sketches. If you can load a sketch, the bootloader is working fine, and shouldn't be having any effect on the sketch itself.