This page is for the original 2011 game. For the 2014 remake, see The Binding of Isaac: Rebirth.
On the options menu, it states F is the key you use to toggle fullscreen/windowed mode. However, this only works on the title menu or in the pause menu. In-game, pressing F does absolutely nothing unless the game is paused. Currently, there is no fix for this.
A fan made fix has been developed to solve this issue on Windows.
For the achievements gained on OS X to be unlocked in Steam, one has to copy and replace the so.sol files as outlined here. The file is located in:
~/Library/Preferences/Macromedia/Flash Player/#SharedObjects/''<Random String>''/localhost/
After extracting it, follow the instructions given in the aforementioned link. Finally launch the game and see the achievements unlock.
Solution: press F, it toggles fullscreen.