Having the same problem.
I did CREATE NEW USER and experienced the same problem with the new user.
When you mention "base files" - what files, in what directory, and what problem is being referred to?
Notes: Originally I was trying to modify the signature I would send out via Mail. I would modify the Font Style, Size, and Color and from what I saw on my screen via Mail 6.2 - everything looked fine. I sent myself an email - hopped over to Google Apps to see how Google saw it - Let me tell you Mail 6.2 and Google do not see eye-to-eye. What I saw from on my screen via Mail 6.2 was not what I Google mail saw
I went into ~/Library/Mail/V2/MailData/Signature and looked at the signature file to see what was being sent. Initially, from a font perspective, there are a lot of assumptions with respect so style, size, and color. Then, in the middle of the signature - where font format changed and became "defined" everything changed as to how Google mail saw it (and the rest of my business clients).
Someone out there has to have figured this out. The few of us that are still baffled would like just a few hints on how to resolve this interesting problem.