Can someone explain what the main differences are between the two?
I'm only concerned about resi or small office environment, so limit of 100 sources for example is not a concern.

Other than one using Coax and the other using category or fiber cabling, what is a real advantage/disadvantage of one vs. another?

Here is what I see:

1. JAP doesn't do interlaced, which is what most of DirecTV stuff is.
2. JAP is little more complicated if sources are not in same location (stacking 500 series switch is required)

1. M3B as no IR.
2. M3B lipsync under certain cases

Seems that M3B has a cost advantage, but sine there is no IR, that needs to be taken into consideration.