Ok, I had a look at the file names and even though you didn’t change them they are incorrect. Its the same case I had, the directory filename follows the new convention, while the rest of the directory follows the old convention.
So a quick fix to trick Sen2Cor in thinking it is the old naming convention is to add _OPER_PRD to the directory name, that it looks like:
S2A_OPER_PRD_MSIL1C_20160807T120222_N0204_R023_T28SCB_20160808T001240.SAFE
That should work, also if you have want to have more verbose messages from Sen2Cor, open the GIPP file (on Windows it is \Documents\sen2cor\cfg\L2A_GIPP.xml) and on the fourth line change Log_Level to ERROR or CRITICAL.