Some thoughts about baseline expectations...
First - if I have an employee who I know has the capability to really handle things when I'm out, I really value that. Having watched many fail, I'd say it's harder than it looks and often the folks who are naturally good at it don't realize how many people are NOT naturally good. So it could well be that while you think it's no big deal, she has had other experience.
That said, some people are effusive thank-you givers. They like making a big deal out of seemingly normal things --- and sometimes that's just how they are. It's certainly better to be excessively grateful than excessively demeaning!
A couple thoughts if it's driving you absolutely crazy:
- Look for effusiveness in multiple places - it may not be just you, the boss may just be a big thank-you giver. Or effusive about a lot of things. Or effusive in particular situations. Look for a pattern. If it's just you, that may be rather weird, but I'll bet you may not have noticed the other cases.
- Take a quiet moment out of the loop and ask if there's a reason. Something like - "I really appreciate that you notice the extra work I do when you're not here, it's great to be appreciated. But it's been pretty easy to do and hardly seems worth all your praise. Is there something I'm missing about the value of how I'm helping? I feel like I loaned you a spare pen and you thank me like I just gave you a sports car." Do it in private and make sure you stay positive about it.
I often use humor in these situations - but that's a difficult and personal choice. I have a big personality and I'm known as a person who likes a good laugh. The humor is never a put-down (of anyone but myself) and aims to be inclusive. But it's a natural response for me to deal with awkwardness. If using humor feels even more awkward, it will seem that way to your listeners, too, so skip it.
A good litmus test is - if all these suggestions seem like too much work to you, then let it go - it's really not a big deal unless it's bugging you, so only you can know how much it bothers you.