I saw that at the end of the last Amazing Spiderman issue Ironman attacks iron spidey. My problem with this is that there is no way in hell Spiderman would be wearing that suit at that time. It's obvious that Pete is aware of the consequences of his actions and that he will eventually have to throw down with Ironman. Spiderman is also aware that the suit is taking information about the extent of his powers, and that Stark's paranoid ass probably has some sort of fail safe devise implanted in the costume. With all this knowldge then, why wouldn't Parker's first action be to take off the damn suit?
Personally I think that Spider-Man has tinkered with the suit to remove whatever safeguards were there. Remember in the previous issue where he thinks something like maybe "I need to check whats being outputted" or something like that. My guess is he takes a look see and discovers something then removes.
Or another scenario is that he trusts Stark too much to think he would do something like that to him. Remember Stark is the guy that took him and put a roof over his head and has been like family to him. Sure Stark may be going too far with this registration thing but in the end maybe Peter still thinks too highly of him to believe he could do such a thing.
The suit can go invisible. Tony explained it to Pete a few issues back, so he was just wearing it at the end of the most recent issue but we couldn't see it until the last few panels.
Anyway, keep this sort of stuff in the many threads in the Spidey forum that cover ASM.