The game seems to have stopped tracking my scoring after I had to unisntall and reinstall due to the program being unable to start. Now, when I do a puzzle it shows my team as being blank, but the points are being counted. However, when I go back to the puzzle selection screen, it shows the puzzle I just did as being unattempted and my userpage shows my last puzzle played being on 7/05/09, and it has been much more recently than that I have completed a puzzle.
This is a known problem that should be addressed in an upcoming release.
One thing you could try would be to re-enter the same puzzle you are in from the puzzle menu. That should force the game to try to send your score to the server. Does your score show up on the webpage if you do that?
So far it has not yet, but I believe it takes a while for the scores to be calculated and posted on the page so I won't know for sure yet. When I reenter the same puzzle my score is still the same as it was when I left the puzzle, but it is not shown on the main menu or on the webpage.
This problem should be fixed in the current release.