Wrong font in PDF opened in Preview

I have a Mac G5-Intel running 10.5.4. The problem is as follows:
I make a figure (a plot) with Igor, save the plot as EPS. I use Preview or "epstopdf" command to get the PDF.
For figures I processed before this problem showed up, the Preview displays the wrong font, but Acrobat displays the correct font (this is the font I selected in Igor when I first made the plot).
For figures processed after the problem showed up, both Preview and Acrobat display the same wrong font.
If I open the EPS version using some other application such as Canvas (a drafting software), the font displays correctly.
If I try to alter the font in the PDF file using Acrobat (full version), the font cannot always be changed because "The compatible system font and the document font may differ and some characters may look different. If the font is not on your system, there will be no way to re-embed it. Do you want to proceed?" message appears. I click "yes" and the font changes to Arial (I had requested Helvetica).
If I then want to change the font again to the previous condition, Acrobat refuses because "The change to a different font was not done because the chosen font and the font encodings in the document differ and could not be resolved."
The problem never occurred in my older Mac Power PC running 10.4. In my new Intel Mac, there was a trouble-free couple of weeks after I got the machine.
The problem doesn't happen when I take my pdf figures to a colleague's identical machine or to my Intel MacBook Pro laptop running 10.5.2.
Any ideas?
Thanks

The problem also affects the same plots when they are part of a Latex output PDF made with TexShop. I thought this is normal, since Texshop uses Mac's PDF Preview machinery to process.

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