I am not familiar with texlipse but, if you have not yet got to the bottom of this I would expect a second compile run should resolve the warnings. For the second run to be effective you need to keep the output files from the first run (especially the .aux file, see below).
1) I assume the package declaration \usepackage{acronym} is in your .tex file preamble.
[If not then it would still work (sort of) in that there would be lots of errors (e.g. '! Undefined control sequence. l.8 the \ac{AL} periodically and the \ac{AM} once.') but the acronyms appear in the text (all unexpanded of course) and the acronym list appears in the acronyms list.]
2) With the acronym package then the following compiles without error but with lots of warnings of the type you report (e.g. 'Package acronym Warning: Acronym `AL' is not defined on input line 8'.):
\documentclass{book}
\usepackage{acronym}
\begin{document}
\chapter{Text sample}
\addcontentsline{toc}{chapter}{Text sample}
Not much to be said here other than to note
the \ac{AL} periodically and the \ac{AM} once.
The second \ac{AL} occurrence, as discussed.
\chapter*{Acronyms}
\addcontentsline{toc}{chapter}{Acronyms}
\begin{acronym}
\acro{AL} {Authentication List}
\acro{AM} {Authentication Module}
\end{acronym}
\end{document}
However, the PDF file does not look correct as the acronyms are rendered as, for example, 'the AM! (AM!)'. The reason for this is that on the first pass of the compiler it cannot resolve the acronyms but by the end of the pass it has written the details into a .aux file with the same name as the .tex file. e.g., for the simple .tex above the .aux file generated by pdflatex was:
\relax
\reset@newl@bel
\@writefile{toc}{\contentsline {chapter}{\numberline {1}Text sample}{1}}
\@writefile{lof}{\addvspace {10\p@ }}
\@writefile{lot}{\addvspace {10\p@ }}
\@writefile{toc}{\contentsline {chapter}{Text sample}{1}}
\undonewlabel{acro:AL}
\newlabel{acro:AL}{{1}{1}}
\acronymused{AL}
\undonewlabel{acro:AM}
\newlabel{acro:AM}{{1}{1}}
\acronymused{AM}
\acronymused{AL}
\@writefile{toc}{\contentsline {chapter}{Acronyms}{3}}
\newacro{AL}[\AC@hyperlink{AL}{AL}]{Authentication List}
\newacro{AM}[\AC@hyperlink{AM}{AM}]{Authentication Module}
A second pass of the compiler can then use the information in the .aux file as it parses the .tex file to generate a complete .pdf file, including, by default, the expansion of the acronym on the first occurrence. On my system this generated the .pdf file as expected and with no errors or warning from pdflatex.
You could use glossaries' \ifglsentryexists macro to define a \provideacronym macro which will only define an acronym if not already defined. Additionally (as in my MWE) you could redefine \newacronym as \provideacronym.
\documentclass{article}
\usepackage{glossaries}
\let\oldnewacronym\newacronym
\newcommand*{\provideacronym}[3]{%
\ifglsentryexists{#1}{%
}{%
\oldnewacronym{#1}{#2}{#3}%
}%
}
\renewcommand*{\newacronym}{\provideacronym}
\newacronym{cd}{CD}{compact disk}
\newacronym{cd}{CD 2}{compact disk 2}
\begin{document}
Some text about \gls{cd}.
\end{document}
Best Answer
You can try this: