The first match includes the second comma, so the second match will start at the third one.

Before s///:     ,  ,  ,  ,  ,  ,  , 6
After 1st pass:  ,,|  ,  ,  ,  ,  , 6
After 2nd pass:  ,,  ,,|  ,  ,  , 6
After 3rd pass:  ,,  ,,  ,,|  , 6
[download]

The | indicates where a substition ended and from where the next pass will search.

Solution 1: Start from the begining instead of where the last match left off.

1 while s{, +,}{,,};
[download]

Solution 2: Use a zero-width match to check for the "closing" comma.

s{, +(?=,)}{,}g;
[download]