I have a level 3 book, I have a hair over 31 levels...

I use the book...

and it doesn't take all the experience.

but doing a "/experience query {name} points" says I have 0 points...

Same thing happens with another player on my server, exact same amount of exp bar filled as me, but still 0 points when the above command is sent

More info... If I put all the experience in the book, then set my experience to zero, then "flip/flop" with the book, the bar keeps the correct levels until I get more experience, then the bar is "broken" again.

Yes I had noticed this during testing, but it actually takes all the experience as you noticed. It's like a graphic bug.
As you also encountered this, I'll try again to figure it out. Thanks for report ;)

That's fixed! Was actually quite easy to solve as it was just a graphic bug because of floating values. I will update the mod a bit later