A temporary workaround is always simply Command-A to select all cells and clicking this convenient button in the ribbon under the Home tab in the Number section:
A more permanent solution is as follows:
Go into System Preferences > Language and Text and click the "Region" tab. If the first region dropdown menu is United States (Computer), this might be your problem. Looking below shows that this region formats numbers without a thousands separator.
This appears to be the result, as you stated, of an OS X update. Instead, set the Region to United States (without the Computer part).
From the Excel Help window:
Display or hide the thousands separator
Select the cells that you want to adjust. On the Home tab, under
Number, click Display the value of a cell with a thousands separator.
Note: Excel uses the Mac OS system separator for thousands. You can
specify a different system separator by changing the regional settings
in Mac OS X International system preferences.
We have just done that, but it appears that Excel continues to ignore the change. Re-install Office and update us with the results.