Flat spot when accelerating from idle

Hi all, been having some problems with a 'flat spot' on my bike for a while now and it's really starting to annoy me. The bike is a Yam XT 125 R carbourated 4 stroke, ~4500 miles on the clock.

The bike runs pretty much fine, has plenty of power, can reach 60mph no problem. Just when the engine is warm, ticking over steadily about 1500rpm (as recommended), and I'm at some traffic lights for example. If I leave the engine ticking over for any more than about 10 seconds and I apply ANY amount of throttle, the engine 'bogs' down a little, sounds like its going to stall, then picks up again.

I've replaced the plug, checked spark (was blue when plug was new, gone yellowish now), cleaned air filter, made adjustments to air/fuel screw on carb, replaced the carb, no air leaks in the snorkle or anything, oil changed about 600 miles ago.

I always thought it would be an air/fuel mixture problem but after having a new carb and still the same problem? One thing worth noting actually is that I didn't have this bogging issue when I'd just replaced the carb. I went for a long ride, and notice the idle was around 2300rpm (choke was definitely off)as apposed to the 1900rpm the bike ticked over when warm but before a long ride. After adjusting the idle speed down to 1500 and richening the mixture screw a quarter turn (i guessed high idle was due to lean running). And i got the bogging back.

The only thing left that I can think of is valves.. but for a 4,500 mile bike is it really likely to be valves out of adjustment?

I can take a video and post a link here if the description is a bit vague.

Any input greatly appreciated!

Thanks