machines certainly will have different base concepts. if they are self aware, then they will in fact, know what they are. they'll think in terms of being a machine, not worrying about pain, or biological processes. they'd likely have less fear of injury or death, as they know that by their very nature, it's easier to repair them. as for thinking "coldly" or without emotion... not necessarily. it depends on how complex their mind is. most likley, if they have a very developed psyche, then, they would exhibit similar patterns to organic beings. Remember, though, there's a different in intelligence and sentience. a machine might be as smart, or smarter than humans, but it could be on the emotional level of a mantis or beetle.
the agents knew that they were software. they were sentient blocks of code. essentially, a software-based neural net. they were able to deal with people in a very human fashion. yeah, they were mean, and operated in a "shoot first" fashion, but they were also quick to deal, and had no reason to deceive.
I highly doubt that the matrix itself has any core software. instead, it probably has another positronic brain at its core that coordinates everything. the entire thing would have to be analog, otherwise it would require the most complex DAC ever devised... for each person.
