Maybe we're missing some side info, but I'm a bit confused about why you suspect the boss is playing some kind of passive-aggressive power-trip game with you.
What's the quote - "Never ascribe to malice that which can be explained by stupidity"? That probably applies here.
IMO, it's bad form to assume the boss is purposely jacking you around, when he/she may very well just be clueless about optimal flight selection (as most people are).
That's probably not a healthy way to begin the new boss-employee relationship, even if you're keeping those thoughts to yourself.
I actually really like her---but she made several comments about how she is very good at saving money traveling--I have booked my own travel for years and its hard to let go of the control. What I detest is as you mentioned in above comment, making someone connect several times to save a few bucks. My thing is aisle seats--I have to sit in aisle seats, and if I have to, will pay out of pocket to get them. but in a few weeks I will be booking my own travel, and hopefully most of the time it will go smoothly. hopefully I can gain status on a few carriers so the seats arent an issue
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BTW, I *also* hate when other people book my travel. It gets messed up at least 25% of the time, and it is rarely optimal.