I charged the battery yesterday, and went to start the NSR today for a quick run in the shed. It started first kick, but it is only running on one cylinder for about 30 seconds, and is difficult to keep it running. After 30 seconds, both cylinders start firing, but I'm noticing that I can only see smoke coming from the newly started cylinder, the one that was initially running stops smoking (or is smoking very little) by this.

What is the likely cause of such a problem? I ran it for a couple of minutes, but the smoke didn't seem to be equalised.
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MC21 Honda NSR250. TYGA 300 conversion.