I have just upgraded to, or more specifically - installed a parallel distribution of, TeXLive-2009.  Since doing so, I have found that typesetting LaTeX does not work correctly when the document references locally held "personal" class, style, bib or other files stored in ~/Library/texmf.  The errors are included below (with some personal info redacted):

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Latexmk: This is Latexmk, John Collins, 2 December 2007, version: 3.21j.

**** Report bugs etc to John Collins . ****
pdflatex: Changes:
Non-existent destination files: 'XXXXXXX_XXXXXXXX.pdf' Rules to apply: 'pdflatex'
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Running 'pdflatex -interaction=nonstopmode -file-line-error-style -interaction=nonstopmode -file-line-error-style -synctex=1 "XXXXXXX_XXXXXXXX.tex"' ------------

Latexmk: applying rule 'pdflatex'...

This is pdfTeX, Version 3.1415926-1.40.10 (TeX Live 2009) restricted \write18 enabled.
entering extended mode
(./XXXXXXX_XXXXXXXX.tex LaTeX2e <2009/09/24> Babel and hyphenation patterns for english, usenglishmax, dumylang, nohyphenation, german-x-2009-06-19, ngerman-x-2009-06-19, ancientgreek, ibycus, arabic, basque, bulgarian, catalan, pinyin, coptic, croatian, czech, danish, dutch, esperanto, estonian, farsi, finnish, french, galician, german, ngerman, monogreek, greek, hungarian, icelandic, indonesian, interlingua, irish, italian, kurmanji, latin, latvian, lithuanian, mongolian, mongolian2a, bokmal, nynorsk, polish, portuguese, romanian, russian, sanskrit, serbian, slovak, slovenian, spanish, swedish, turkish, ukenglish, ukrainian, uppersorbian, welsh, loaded. ! LaTeX Error: File `gregsarticle.cls' not found. Type X to quit or to proceed, or enter new name. (Default extension: cls) Enter file name: ./XXXXXXX_XXXXXXXX.tex:2: Emergency stop. l.2 \usepackage {amssymb} %maths^^M ./XXXXXXX_XXXXXXXX.tex:2: ==> Fatal error occurred, no output PDF file produced! Transcript written on XXXXXXX_XXXXXXXX.log.

Latexmk: Missing input file: 'XXXXXXXXXXXX.cls' from line

'! LaTeX Error: File `XXXXXXXXXXXX.cls' not found.'

Latexmk: Did not finish processing file: 'pdflatex' did not make 'XXXXXXX_XXXXXXXX.pdf'

Latexmk: Errors, in force_mode: so I tried finishing targets

Application 'Skim' not running
The file /Users/XXXX/Desktop/XXXXXXX-XXXXXXXX/XXXXXXX_XXXXXXXX.pdf does not exist.
execution error: Can’t make file "Macintosh HD:Users:XXXX:Desktop:XXXXXXX-XXXXXXXX:XXXXXXX_XXXXXXXX.pdf" into type alias. (-1700)

error number 256 opening viewer

Found 0 errors, and 0 warnings in 1 runs

/Applications/TextMate.app/Contents/SharedSupport/Bundles/Latex.tmbundle/Support/bin/latexmk.pl -pdf -f -r /tmp/latexmkrc "XXXXXXX_XXXXXXXX.tex" exited with status 12

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Now, I initially thought that this might be a problem with the TexLive distribution.  However, when switching between the 2008 and 2009 versions and using TeXShop as the frontend, there are no problems in either version; TexLive-2009 recognizes files under ~/Library/texmf and parses them correctly.  The next thought was that it was an issue with different versions of latexmk.pl - but TeXShop doesn't use that script unless it is specifically added on; it's not part of the basic distro.

Quite frankly I'm at a loss to suggest what the cause could be for this behaviour.  On the other hand, there is a fairly simple workaround - just include the necessary class and style files in the directory of the .tex document from which they are referenced.  the ./ path seems to work without problems.  Of course, this defeats the purpose of having ~/Library/texmf, but at least it works.

Hopefully someone with more expertise with the guts of the LaTeX bundle and/or TeXLive will be able to figure this out.