You can also play levels from the level database in the editor (I assume you are just playing the built-in levels) and with those points unlock stuff as well.
Very stange that any of our Flash games would just stop working, haven't heard this happen before. Have you tried a different Flash player? Or move the DD:MIA.swf to another location on your computer (Flash Player stores the settings etc. of a .swf file based on the .swf's location on the computer)?