A number of years ago I gave this over as a talk during a Shavuot Program at Cong. Mt. Sinai in Wash Heights...
Here is a brief summary
The difficulties -
If we presume that ALL Taryag Mitzvot were given literally at Mt. Sinai, then:
A. How did at least two mitzvot first occur in the midbar
1. Pesach "Sheini" ?
2 Y'rushah for B'not Zlaphchad?
B. How could the BeHaG, one of the first "listers" of Taryag include so many Mitzvot mid'Rabbanan?
C. How come apparently no lists of 613 Mitzvot were kept by Hazal?
D Similarly - how come Hazal were not concerned when arguing if a given mitzvah was one or two? After all it should have messed up their individual lists?
BE"H I will give my approach from Mt. Sinai and then another possible hypothesis