Have had this on the Triumph and GS; and I think (corret me is wrong) Toph had it with his old Honda and it was down to debris in the fuel blocking jets.

Sounds like the float jet isn't closing, causing the bike to flood on one pot. This will clear as you draw the fuel through at high revs.

The quick answer is to drain the float bows a few times and try to flush it out (I did this on the GS and it cured it) the proper way is to remove the float bowls and clean out the jets and bowls.