Going back to the original post, there does appear to be a bug in the GIF reader in PDF::API2, which causes it to decompress larger size GIF files incorrectly. I managed to trace through and fix it for my project. The relevant library file GIF.pm, version 2.0, 2005/11/16 contains an error in line 135. The patch is as follows: 
C<<
 135c135
 <         $bits++ if($nextcode == (1<<$bits));
 ---
 >         $bits++ if($nextcode == (1<<$bits) and $bits<12);
>>

[download]
I will submit this bug/fix to the package maintainer but in the meantime this post should help people who are stuck get their program working again.

In reply to Re^2: Including GIF image into PDF (using GD::Graph and PDF::API2 libraries) by Anonymous Monk
in thread Including GIF image into PDF (using GD::Graph and PDF::API2 libraries) by asulkin

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