Stoner built the prototypes for ammunition loaded with IMR powder, which burns significantly cleaner than ball powder. In fact, one of the initial problems with the rifle was that the soot and gunk from the Army's ball powder ammunition built up quickly and required frequent cleaning. Further, the Army did not let Stoner and his team know about the use of ball powder until well after problems had cropped up in actual use.
Ball powder has other side effects, particularly the powder being used in the early loadings. These loads produced higher gas pressures, which caused faster cycling and higher cyclic rates of fire. This was addressed with a much heavier buffer than the original.
In the latest edition of E.C. Ezell's "Small Arms of the World" that I have (it's about 10 or 12 years old, and no I don't have the edition number handy-I don't have all my books out right now) there's a nice long discussion about the development problems with the M16, including the chamber corrosion issue and of course the lack of coordination between all the different parties in what was going on and when.