In a few episodes of Dollhouse,
Echo is activated as a sort of sleeper agent
to send messages to Paul Ballard in an effort to keep him on task in his mission to locate and bring down the Dollhouse.
During the series, it is revealed that
Mr Dominic and Boyd Langton are both traitors. Dominic is actually NSA and Langton is actually one of the heads of the company.
Since the messages sent to Ballard end when
Mr Dominic is exposed and sent to the attic,
it is heavily implied that that person is injecting extra programming into Echo, but
on multiple occasions, he has tried to kill Echo, or at least expressed wanting her sent to the attic. It also doesn't seem like Dominic would have the technical know-how to correctly hack the imprinting device or alter Echo's programming. There is also the issue of November delivering a hidden message to Paul after Mr Dominic has already been sent to the attic. Boyd might have the technical know-how to hack the imprinting chair/process, but sending messages also wouldn't make sense since he would effectively be bringing more attention to his own company.