Hi Paul, I also have an MC18 and discovered my bike was doing exactly the same when starting it up.
I found I was leaving the choke on too long so it was flooding the top cylinder.
Now I when I start the bike on full choke I immediately shut it down to half choke (in a matter of seconds) and about 5 seconds later shut the choke off completely. It's just a case of playing around with the choke until you find the set up for your bike without flooding it.
Hope this helps, it definitely stopped my bike from running on just one cylinder.
Cheers & Good Luck.