Toilet drain mystery

Hi,
My wife and I successfully installed tiles one of the upstairs bathrooms so we decided to tackle the one on the basement. After we took the old vinyl floor we discovered that there was a chunk of concrete missing by the toiled drain hole.
In order to better illustrate this I have taken some pictures and posted them in the following URL: http://picasaweb.google.com/gino.serpa/Toilet
There you can see the hole about 1.5 inches deep and a few inches in diameter. It looks like somebody chiseled it away. We are not sure whether it has something to do with the crack that comes form the left or whether it was a mistake. The vinyl is the original so we assume this was done during the original construction of the house. ANother thing that bothers us is the different color of the area surrounding the drain hole (last picture), was this leaking? would it be a problem if we just patch the whole with cement and proceed with the installation of the tile? Any help, advice or guesses as to why this hole in the concrete is there would be extremely appreciated.
Thanks in advance
Gino

Looks like they had to chip out the concrete to fix a messed up rough in...
Looks like an offset flange...

Yes that is an offset flange. Any chance that this is the reason they had to break up the concrete? I mean to make room for the offset flange.
How about the darker area is this typical of a leak due to poor fitting to the wax ring.
Thanks for your response by the way

How is the level of the flange compared to the floor? Use a straight edge to check.

The concrete was probably chipped out when they installed the offset flange. Clean any loose debris out of the hole and fill it with Hydraulic Cement. You can then secure the ring with Tapcon screws. If that was a severe leak or, for any length of time the painted steel flange would have been rusted out.