The fault for this lies somewhere within:
pnetlib/runtime/System/Private/NumberFormat/CustomFormatter.cs

One issue from what I can see appears that:

while (formatindex >=0 && format[formatindex] == groupSeparator)
{
scale += 3;
--formatindex;
}

Given the input of "123456" and format of "#,#", this will never get called with a "#,#" format as in this example, formatindex is set to length of the format minus one, so length = 3 - 1 = 2, the char at position two (array of 0 = '#', 1 = ',' , 2 = '#').  The second test condition of the while fails.

Setting the second test condition to a != test allows the decimal to be placed in the correct position in the numeric value passed in, however the padding doesn't seem to take place.  While the MS.NET implementation would show 100.000 in the test case, I'm getting 123.<nothing> while using the != above.  The MS.NET docs on numberformatting isn't exactly clear as to if the padding will be zeros or if the second number placeholder will be the remainder of the input numeric value (i.e. .456).  I'm going cross eyed looking at this method, a fresh set of eyes may be good.  If not, I'll revisit it at a later date.