As I'm sure you probably realize, the isolator and the generator starting problems are not really related to each other, at least not directly.
Does the generator spin somewhat slowly when it does turn--does it seem to have a little trouble getting through the compression stroke? If so, I would guess that you have a problem with the generator's starter motor. On my generator, at least, the starter (a permanent magnet motor) had four poles, and hence four brushes, two positive and two ground. A failure in one of the brushes would and did result in it working, more or less, but marginally with approximately half the oomph it should have had. (It finally failed due to an attempted start on a cold winter day where it didn't have enough torque to pull through the compression stroke and, due to my pig-headedness in trying to hard, got a burned out coil or two. Replacing the starter was a pain, but the new one does work much more energetically and effectively and reliably.)