In the episode "A Race Through Dark Places", Talia Winters joined hands with the rogue telepaths to cheat Bester and gave him the illusion that he had the rogue telepaths taken care of. How could Bester be cheated, given that there is a sleeper or spy implanted by the Psi Corp into Talia Winters (See episode "Divided Loyalties"? Even if this sleeper allowed Winters to commit her treacherous act against the Psi Corp, this "spy" within would surely have reported her treachery to Psi Corp. How could Bester not know?
Bester is high up in the Psi Corps, but he's not at the top. We get a little better view of his position within the Corps in the episode "The Corps is Mother, The Corps is Father". While we are never shown all the roles he plays in the Corps, most of what we see of him shows that he's a highly competent field agent.
The Corps may be small compared to the population of humanity at large, but it's large enough to for there to be different projects run by different groups that don't all talk to each other about everything. Some reasons for the separation might well include practicality (no one can know everything going on in an organization), and deniability (what one doesn't know, another can't find out).
From the JMS speaks portion of the Lurker's Guide page for "Divided Loyalties":
[Question:] Did Bester try to befriend Talia because she was Control? (cf. "A Race Through Dark Places")
[JMS:] You're assuming Bester knows everything. Also, Bester's interest may have been more...carnal than PsiCorp oriented.
We also see in the episode "Epiphanies" that he's not let in on the entire plan that he's being involved in. As shown in the episode "Ship of Tears", he never knew what the Corps did with the 'Blips' like Carolyn they had.
This doesn't show that Bester definitely wouldn't know if Talia's sleeper personality reported back to the Psi Corps, but it should show that he's not in a position to know everything that goes on. If Talia's sleeper personality reported back, he simply may not have been told. Also, even if he knew, there's no reason for him to act on the information (and therefore show us that he knew), because it would compromise a valuable information-gathering asset.
This also depends on the sleeper personality reporting back. It's certainly possible that it did, as in "Divided Loyalties" Lyta identifies the personality as Control, who did play a part in "A Spider in the Web". It's also possible that Talia's sleeper personality simply remained quiet and bided its time, while Talia became more involved in resistance activities. We're never given any indication either way.
We shouldn't assume that the split personality aspect was in play then at all. It was a justification to get her off the show when the actor wanted out.