If we're looking for other reasons that Dora's attitude towards Faye has changed a bit...well, maybe she is growing a bit tired of her abrasiveness. At one point it was oddly charming and endearing, but over the years, perhaps it's become more grating.
I think making her the assistant manager is also a factor here. On top of increasing her sense of feeling betrayed when Faye broke the "no drinking at work" rule, there was also the incident where Penelope and Cosette were willing to immediately quit upon being told about it. While she managed to allay their concerns and smooth things over, maybe that was a bit of an eye-opener for Dora; until that moment, maybe she didn't really think about how Faye treated other people, or didn't consider it a problem because Faye didn't treat her as abrasively as she does other people (what with being her employer, and all).