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I've had something similar with a '86 Tenere, which has the same carburettor, but probably a different inlet system / air filter arrangement.

Checks:
1. Make sure your air filter is is very, very clean. Is it washable on your bike? If so, wash 3x times in petrol, let dry, and oil lightly with engine oil or air filter oil.
To test the difference, test it without air filter see if the problem goes away.
2. 'Synchronisation' of the second (RH) carb. As far as I know there has been an official modification from Yamaha. The valve in the mixture channel to cil head should not start opening at 5 mm lift of the primary slide, but @ 7 mm. Adjust by putting 7 mm drill under slide LH carb, and adjust screw till butterfly valve just opens.
3. Do not touch the jetting. Yamaha is king in this, no fiddling! Use stock jets, and make sure the needles are in the correct positions:

- LH carb: needle 5C37, clip in 4th notch from top
- RH carb: needle 4A71, clip in 4th notch from top

Use the original jets.
4. Check the vacuum operated slide of the seconf (RH) carb: does it move easily and smoothly, does it return to it's rest position aftr opening?

Your problem has probably to do with too rich a mixture at constant speeds. Rereading the above, I expect the most from 1 and 4, so try them first, provided your jets and needles are at factory settings.