All 996's came with two injectors per cylinder. Before the 996 model, only the SP and SPS bikes had dual injectors. However, those earlier bikes use the larger P8 computer which is capable of firing the injectors sequentially, meaning that the second injector sprays only at the higher engine speeds.
The 996, on the other hand, is controlled by the smaller 1.6M computer which is incapable of firing the injectors sequentially. So the engine does not run well with both injectors firing at the same time, especially at low rpms where spray durations get too short to get good spray patterns. The fuel dribbles out.
According to FIM, dual injectors are not needed unless you're making more than 120HP, and so they have developed a single injector chip for the 996.
Read more about it here:
http://www.moto-one.com.au/performance/996eproms2.html This is a quote from FIM's site:
"We have two UltiMaps for the 996 Biposto '99/2000 model. There have been many problems with these models spitting on low throttle or cruise at low speeds. We have finally made a chip which cures the problem (type UM222), but requires that one injector be disconnected from each cylinder. This is because the 996 has two injectors hard-wired in the harness and we can't switch one off like we can with the 996SPS or early 888 computers. The benefit is that the single injector spits more cleanly at low durations than two injectors do ( because they have only half the time each) and idle and low throttle repsonse is heaps better. We remapped a 996 with this mod and the difference is incredible. We do sell a twin injector verison of the same chip (type UM221), but in most cases the UM222 works better, and is worth the effort."
http://www.fuelinmoto.com.au/ According to Brad Black:
"The UM222 single injector EPROM cures the 996 misfire that occurs when you roll the throttle open at 3,500 rpm. The UM222 is only for models fitted with strada cams, not models having SPS etc. cams. Typically it happens when you get it to 3,500 rpm. Duh duh duh duh vroom. Not 3,000 rpm. Not 4,000 rpm.
THIS IS THE ONLY MISFIRE THE UM222 SINGLE INJECTOR EPROM CURES OR IS INTENDED TO CURE."