Is your item a bundle by any chance?    I'm having an issue where it doesn't increase the tax if you change the quantity on the bundle.  At forst I didn't realize what was going on and why my sales tax filing was always incorrect.   It's been a nightmare. I've paid a ton of penalties for being late trying to figure out where things went wrong.

Anyway, I wouldn't expect any decent response on here.  The QB team will not be of any help to you.