I found that the New TX math font newtxmath could not displace underbrace, see: latest Texlive 2012

The correct underbrace with default CM font:

It's weird that it works well when I test it with a simple tex file.
\documentclass[12pt]{book}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage[T1]{fontenc}
\usepackage{newtxtext, newtxmath} % new TX times
\begin{document}
\begin{eqnarray}
\frac{\sin^{2}\vartheta}{\Theta_{lm}(\vartheta)}\left(\frac{\partial^{2}}{\partial\vartheta^{2}}+\frac{\cos\vartheta}{\sin\vartheta}\frac{\partial}{\partial\vartheta}\right)\Theta_{lm}(\vartheta)+\sin^{2}(\vartheta)(l(l+1)) =\underbrace{-\frac{1}{\Phi_{m}(\varphi)}\frac{\partial^{2}}{\partial\varphi^{2}}\Phi_{m}(\varphi)}_{blabla} \\
P_l (x)\equiv\frac {1}{2^l}\sum_{k=0}^{\lfloor l/2\rfloor} (-1)^k \frac{(2l-2k)!}{k!(l-k)!(l-2k)!} x^{l-2k}\\
\iint_\Omega \frac{x^2+1}{2y}dxdy = 0
\end{eqnarray}
\end{document}
But it won't work with these packages used for my report:
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage{graphicx}
\usepackage[table]{xcolor}
\usepackage{enumerate} % numbered items
\usepackage{color}
\usepackage{booktabs}
\usepackage{threeparttable}
\usepackage{multirow}
\usepackage[UKenglish]{babel} % ngerman: "a "s "o "u
\usepackage{subfigure}
\usepackage[colorlinks]{hyperref} % ref
\usepackage{natbib} % bibtex
\usepackage{cases}
\usepackage{algorithm}
\usepackage{algpseudocode}
\usepackage{wallpaper}
% | * * * * * * * * * * * * * * * * * * * * |
% | fonts with math support |
% | * * * * * * * * * * * * * * * * * * * * |
\usepackage[T1]{fontenc}
\usepackage{newtxtext, newtxmath} % new TX times
\usepackage{esint} % Alternate integrals signs
\usepackage{ngerman} % after package mathdesign !
The rest packages and setting are for page layout, margin, etc.
I am sure newtxmath conflicts with some certain packages, How to figure this out?
Partial solution: Putting esint before newtxmath will eliminate this issue, but it produces the unchanged \iint symbol:


newtxdo you use? – mafp Jan 9 at 19:02cmex). i would then unpack the.tfmfile for that font withtftopl. the documentation for that program (texdoc tftopl) is going to be useful. what you want to look for is the "math extension scheme" which will have a recipe for starting, extension, middle, extension, ending pieces. the character cell location in the font is wrong for the extension piece. replace that location value by the correct one (it is probably the same as the one for\overbrace) and repackage withpltotf. – barbara beeton Jan 9 at 19:06.tfmfile if it contains an error. it's the "original" method, in use for 30+ years. there may be other methods now to patch.tfmfiles, but this is the one i've used successfully in the past. and it does seem that you found it was not a problem with the font itself, but with incompatibilities when using another package. – barbara beeton Jan 9 at 20:45