Unfortunately the sig-alternate
class uses a peculiar1 way to set the document fonts.
In particular, the \texttt
macro selects the font family aett
(which belongs to a definitely obsolete package) at size 9pt, independent of context. So you have two problems.
Use a boldface version of the Typewriter font.
Increase the font size in section titles.
Solution to problem 1
\DeclareRobustCommand{\ttfamily}{\fontencoding{T1}\fontfamily{lmtt}\selectfont}
Solution to problem 2
\DeclareRobustCommand\sectt[1]{{\fontsize{13}{12}\bfseries\ttfamily#1}}
Example document
\documentclass{sig-alternate}
\DeclareRobustCommand{\ttfamily}{\fontfamily{lmtt}\selectfont}
\DeclareRobustCommand\sectt[1]{{\fontsize{13}{12}\bfseries\ttfamily#1}}
\begin{document}
\section{Algorithm \protect\sectt{FSG}}
Algorithm \texttt{FSG}
\end{document}

Newer problems
Due to how the class is written, you won't be able to make a table of contents if a command such as \sectt
appears in a section title. But this would happen also with \sqrt
and other seemingly innocuous commands
The editors of the conference to which you're submitting the paper may not be happy with these changes.
1 The adjective "peculiar" should be read as "blatantly wrong".
\texttt{something}
typesets "something" in CM Typewriter.sig-alternate
documentclass, but I am not saying a thing about fonts and stuff like that. The size of the typewritten text, however is noticeably smaller than the rest of the section title.sig-alternate
class that's written in what I wouldn't define good LaTeX programming. :(