Which Updates?
RMKboxer, which update did you have done? The piston, head, and new ecu map reflash? If this is the update you have had done there is another new map flash for the ecu to help with the midrange bog, burp, pop, or back fire and hard hot flooded starts.
The old map update program is too lean in the midrange and can burn down the motor if you just hold it steady at mid throttle. The new map is polaris's new fix and it helps according to the new posts on the 4ms. Another choice or option would be to install a power commander five from jim at dynotech.
This should fix your concern unless you have something else wrong? Like sledhed said if you do not have the orignal can or slp can on the sled the dealer may inform Polaris and you may have your warranty coverage voided. Also becuase the engine is so lean in the midrange the burned hole in your can will happen when the can casing is thin and the engine too lean for too long.