The Footprint Analyzer only works if you never used the terminal before. So putting one on after using a terminal and then using the terminal again doesn't help.
That's a good point, and something which should really be fixed. Ideally you
should benefit even on a later connection if you didn't scan it before, but rather than have a separate indicator for whether or not you'd connected with an analyzer before, at the time of implementation I took the easy route and just checked whether you'd connected to that machine at all before, and only checked for analyzers on the first hack (successful or not).
I'll change that behavior by adding a dedicated value, and also have it store the highest analysis level you've performed on it, on the rare chance you later attempt to re-hack the same machine with a more powerful analyzer and it can reward you with the difference.