Compubox is literally two guys with a clicker attached to a laptop who count the punches in real time (see picture below). It's something we should always take with a grain of salt, especially when there are flurries of punches thrown it's nearly impossible in real time to see exactly which ones land which ones miss.
A good example is Calzaghe vs Hopkins. Compubox had Calzaghe landing something like 208 punches total. I've seen a slow motion replay of the entire fight someone made with all the punches counted and Calzaghe landed something like a total of 40-60 punches or some bullshit like that. It's amazing how inaccurate compubox can be.
Now, that isn't to say pacquiao didn't land/throw more against Marquez, just saying.
If compubox really wants to have credibility they should have a live unofficial punch count during the fight, then within the next couple days they should re-watch the fight, with the luxury of watching on a TV and the ability to slow it down if need be, then release official numbers.
Compubox