I guess first of all we need to know what the laser power is as specified as by the manufacturer. For instance, should the red laser have a specified power of 500mW, 800mW or perhaps a 1000mW?
Also, you can't accurately measure a modulated beam. Any pattern you project will be modulated and have blanking. To measure output accurately you will need something like Stanwax's 'ILDAGem', this will allow you to supply your lasers with an unmodulated 5 volt signal. Other than that in LD2000 (if you have it) you can go into the abstract generator and project a white circle, reduce this down to a single spot and aim it at your thermopile. This is the second best option.
Once you know you are dealing with an unmodulated beam we can work from there to diagnose your problem 
Cheers
Jem
Quote: "There is a theory which states that if ever, for any reason, anyone discovers what exactly the Universe is for and why it is here it will instantly disappear and be replaced by something even more bizarre and inexplicable. There is another that states that this has already happened.”... Douglas Adams 1952 - 2001