Mrs. Mooney has always kept a close eye on her daughter Polly's interactions with her many male boarders. These men invariably flirt with the pretty young lady, but as such behavior never actually leads to anything, Mrs. Mooney lets it go on under her roof without getting involved.
However, when it becomes clear that there's something more than just harmless flirtation going on between Polly and Mr. Doran, Mrs. Mooney is initially concerned enough to think about sending Polly back to her previous job as a typist in an office. Yet Mrs. Mooney doesn't make a move; she simply watches her daughter's blossoming relationship from a distance and keeps her counsel.
Polly knows that she's being watched by her mother. But what really disturbs her is Mrs. Mooney's "persistent silence" on the matter. And Polly is becoming more and more uncomfortable with her mother's silence. She senses correctly that she's just biding her time before getting involved. That's why Mrs. Mooney's "persistent silence could not be misunderstood."
Polly knows that at some point, her mother will intervene. The question is when. Polly is also in the dark as to what her mother will say to Mr. Doran when she judges the time is right. That Polly doesn't yet know the answer to these questions is what's making her so incredibly uncomfortable.