I cleaned my ~/.lyx and started fresh.

I exported to .tex in Linux and in Windows and the results are the same
in terms of .tex file.

I noticed that the .pdf file that is created in the imagens directory (the .eps 
logo converted to .pdf) had different file sizes. I opened the two files and 
they are really diferent and it is that that is causing the problem.
So the issue is with the tools that lyx uses to convert the image from eps to 
pdf.

In windows my instalation uses eps2pdf. In linux in lyx i see no
converter from eps -> pdf so i assume it is using the standard ps2pdf13

-- 
Pdftex 2007-12ubuntu1 produces incorrect PDF
https://bugs.launchpad.net/bugs/124720
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