My bike likes to do it in 2nd, 3rd, and 4th gear when just rolling along in traffic and occasionally when at idle at the traffic light. It just doesn't feel like it's harmless, it has do be doing some damage or causing premature wear on something. I'm trying to understand why the bike hiccups like it does. Throttle on and all is perfect.

 

Synched carbs?

I get the occasional carb fart maybe once every month or so if I'm blipping the throttle while pulling into a parking lot or something but never thru the gears.

 

Lean mixture to pass US emissions is most likely cause. It's more noticeable with big twins. My BWM R100RS would have carb backfires like haknslash described. You've got huge 48 mm carbs that prefer to breathe at rpms higher than 3000 while crusing, but I agree with haknslash that it shouldn't backfire under acceleration.

And the carb backfires won't do any damage as long as you keep an air cleaner in the air box, otherwise you could get a fire.

Just open the throttle a little more and enjoy.

 

Good tuning will dial this out, my bike does not do it now that everything is set right.

 

Typical lean backfires, the lean mixture brun slowly and dwells in the chamber igniting the intake when it opens blowing trough the carb throat messing up the next intake charge.
Fix : shim the needles or lower the clip (DJ needles) one notch.
Or use the stock cans
Chances are that the mains are too small too (lean, white carbon deposits on plugs), a full jetting is in order.