When the tire was replaced and balanced, did you ask the mechanic to see if the rim was within factory spec's? A good shop can check the rim's run out to see if it may be slightly bent. This can also be done with the tire on the rim, but you will most likely want to remove the tire and rim from the bike and hand it to a mechanic, it may be cheaper for you this way if you decide to go this route, but ask the shop first. Another suggestion is be sure whoever does this for you, is good at checking a rim for proper run out, don't rely on some rookie, it's your money, make sure the person doing your work knows his trade.
That's what it sounds like to me, especially if it's always been there. Probably wasn't torqued right initially at the dealer when the bike was set up.
