Virtual Dyno also takes into account the HP lost to drag. On the dyno you eliminate these factors and will it will throw the numbers off when running those logs through Virtual Dyno.
Also you are using non-real world conditions ... these will always produce slightly different results in a pristine environment. Virtual Dyno will be close to those numbers but the curve may be slightly different from differing conditions. Virtual Dyno will give you numbers from the real world vs the ideal world.