Simple answer, it was Janeways monthly 'special lady time'.
Forgive me, for I have sinned and bumped this thread. But ARE YOU SERIOUS
So, I work in video game QA, and we frequently have younger folks coming in on the summers each season. Anyways, a young man who I can only describe as a "bro" was severely annoying a female with a somewhat prickly disposition over the course of several weeks. One day, the woman snapped and lightly beaned the fellow with the backing of a Wii Remote (this is the sort of thing that could only occur in game QA). Granted, not a good thing to do. But the fellow spent the next hour grousing at the top of his lungs about how the "bitch" was "CLEARLY ON HER PERIOD" and turning to me and asking me if I thought she was on her period.
Finally, the other females in the room had heard quite enough and that was that. I don't like to sit around and wave that tired old sexism flag, but damn. I take equal issue with those stupid keychains and shirts about PMS because looking at them lowers my IQ. I make "silly woman" jokes all the time, but entirely on a joke level. But when people use PMS even partly honestly as an argument for a real person or fictional person it just drives me batty. I guess a woman can't be upset unless she's on her period? lolwhat? Perhaps she's just, you know, mad. Because she's human. Maybe something bad happened. Bad disposition. Constipation. Jerk. But, no, no, the silly woman is just suffering from PMS and can't control herself because she's too stupid.
Oh my goodness, I'm sorry for the rant but...but wow.
On topic!
Of course people should have problems with Equinox II. What Janeway was becoming throughout the episode was bad news, and the episode was written so the viewer would slowly back up and realize the hero was starting to become a bit like the villain. I recall watching this episode rather dispassionately on its original broadcast and was like "Oh, I get it, she almost became like Ransom but his death helped her find herself again. Okay."
She was supposed to be wrong, despite what someone said about "never having the woman be wrong" malarkey. Good. Glad to see a few chinks in the armor. Chakotay and Tuvok should have teamed up and held her back - in a way, Chakotay did. She may not have gone so far as to commit murder (I honestly doubt it) but Chakotay did the right thing in stilling her hand all the same.
She was not moping at the end of the episode because she was sunshine and flowers about what she almost became. She was probably scared of herself. Thankfully, she was able to pull back from the brink - something else the episode tried to get across. Rudy bounded over that brink and didn't look back until he was about to die in his silly little "sacrifice." Janeway did not.
Heck, Chakotay was glaring daggers at her in that final scene with the plaque, even though they were trying to come together and play nice. (that's also the scene that made me a J/Cer initially...

A follow-up would have been great, [insert some tired comment/argument about the nature of self-contained episodes], but alas.