Not sure how it applies to the 550 models, but the 750's had a safety switch system where the bike had to be in neutral or the clutch pulled in for the electric starter to function. (There are usually wires going up to the clutch lever) I've noticed some bikes are finnicky about neutral.... some always click right in, others you need to haggle with. Is the clutch disengaging fully? Is the neutral switch seated properly in the bottom case? This diagram might help re the electrics. Not sure if it applies to your model, but it gives you something to look over. Again, this is for a 750, but I don't think it's much different. I'm sure someone will speak up if it is!
I hope this is of some help.