My 2003 did this exact thing.It turned out to be the connection on the little wires that are on the coil.They wore loose and I had to re-crimp them down.

 

1000 miles on a 06. I'd bet the carb is just alittle gunked up.

Ya need to ride it more and use stabil in your gas.

 

just a long story behind this bike and the reason it is over 2 years old and only 1000 miles

my daughter bought it oct 06, took the course and all.
we road it some during oct and nov
then winter
then between the job which required a car, and the fact that she liked to drink and party, she just didn't ride it that much (shows huh)
i took it out a couple times, but it didn't get that much use - she was kinda funny about loaning it out
last oct she got transferred and left the bike with me
said go ahead and ride it when you want
so i put 600 on it just buzzing around. i would use it on the shorter quick runs or for a shorter ride in the evening (shorter could be one to two hours)
my ultra i used for the whole day trips

so yeh - it could be just non use or gummed up carb

and hey - thanks sportypig for those articles

so

 

and don't forget to remove the negative cable from the battery first.

 

ive got the same problem with our 04 XL 883, backfiring thru the carb the moment you crack the throttle-moving or dead stop. never on de-celleration. just got $500 lighter and its still doing it. had the intake gaskets replaced, had 45/170 jets put in, platinum plugs,had the air/fuel screw adjusted,tried both hi and lo octane gas, and still its doing it-hot or cold. keeping the enrichener on almost stops it, but then I leak gas/oil out the air filter courtesy of the breather/open air filter. Ive got an S&S super air filter, drag pipes,jets and plugs, just turned 13K mi. isnt american quality great?

 

i had burps on a S&S i used seafoam on guys here tol me about worked pretty good.
awhile back i had a some unknown azzhole sugar my tank and that caused backfiring n sh-t so i popped the carb off i hand scraped off the sugar build up inside the carb opening. good thing whoever did that didn't know sugaring a gas tank is a wives tale for the most part just a **** off