Sounds to me like there was still just a little bit of air in the system even if you thought you had everything bled out. I've had this happen many times over the years on many different brands of machines. The one thing that seems to be consistant between all of them is that I really thought I had the system bled, and one shot of ether keeps it running when it will not do it otherwise.
I had one a few years back that I bled the fuel system, got it running and drove it around for about 5 minutes. The man came to pick it up and got half way down the drive when it died. We bled it again and this time he got to the end of the drive with it and it died. All total we bled the system a total of 5 time, along with the fact that I drove it around for a few minutes before calling the guy to pick it up, before it ever actually ran like it should.
That said a shot of ether will not hurt an engine, regardless of what many would like you to believe, at leasrt not if it's done in moderation. If it was any diffrent do you honestly think that the mfgs would offer an ether start setup on a brand new engine? Heck even 10 years ago they offered them for the electronic engines that were controlled by the computer. I checked into one for my truck since I often work out of town and park in motel lots where I can't plug in. Unfortunately that setup cost both arms and at least a leg and half of the other. In the end I wound up with a Kim Hotstart system that I operate manually by pushing a button when it's needed. The main thing with ether to insure the engine is turning over so it gets sucked into individualk chambers as a mix, not straight ether, and use it in moderation so the engine doesn't sound like it's going to fly apart as it hits. Do it this way and you should never have any problems.