We see this a fair amount. There are several things which can cause this. But most often, we find that people are lugging the engine. Coming off a low RPM V-Twin sets your ear to hate the 4,500-5,000 RPM that the Spyder is designed to run. Some will go to 6th gear at much lower RPM and then twist the throttle to accelerate without dropping the 1 or 2 gears it really needs to get the engine into its power band. Because the 1330 will do it, people get the idea that it's OK.
I am not saying this is you. Just throwing things against the wall to see if something sticks.
Over time, lugging the engine will carbon up components and clog the fuel injectors. Not to mention possibly damage the clutch plates. Injectors need to be spraying an extremely fine mist to be effective. The issues are most notable at lower RPM. As RPM increases, the injectors are flowing more volume and the restriction is less detrimental.
Things like SeaFoam are fine for maintenance of a clean system. But to clean a partially clogged injector, you need a better alternative. For this, I recommend Chevron Techron. There are others such as Lucas and Red Line products. If the restriction isn't too bad, one of these can get your injectors back to where they need to be. If not, then removal and a good sonic cleaning will be necessary. If you're going to go that deep, changing your spark plugs at the same time is highly recommended, even if the current plugs are still good.
I hope this helps. But for long term happiness, keep those RPM's where they need to be. You don't always need to be in the 4,500-5,000 RPM range, though this is a good rule of thumb. If you're cruising at lower speeds in 1st, 2nd, or 3rd gear, then 3,500+ is fine. But if you want to accelerate, drop a gear first when you are in this range.
Running straight gas when you can is also a great idea. Especially if your Spyder sits for periods of time. Many stations now have OFF HIGHWAY or Recreational Fuel. It costs more money, but so does replacing or servicing expensive components.
One last thing. It doesn't hurt to let your motor idle for 30 seconds or so before shutting down, especially after a particularly hard or hot run. This allows the coolant to circulate, giving the injectors and spark plugs a chance to cool a bit so they don't go on to bake after shutdown.