When I save eps file as a PDF it loses whole colours, but I can see the colours in preview and if I open the PDF in Photoshop. What is going on?

Has anyone else encountered this? I want to save a 2 colour logo (CMYK) as a print ready PDF but when it opens in Adobe Acrobat the black is missing or the green is missing. I can see all the colours there in preview and if I open the PDF file in Photoshop, all the colours as as they should be!!!

No.. sorry.. it does not seem possible effect .. if you can write you must be able to read..
Are you using the TC with user profiles?
What security are you using for disk access?
What happens if you do turn on full guest access to read and write.. ?
When the Mac that can save but cannot read does drop the file onto the TC,, can the other Mac's see that file? In other words is the file really there.. has it copied correctly. I still think if it has copied and you cannot read it back there is some permissions issues.
Try creating a new user on the Mac that has issues.. and see if the new user and read and write correctly. Make sure the new user has at least equal rights as the users on the Mac's that can read and write without issues.
Your intial question suggested this problem was spread over more than computer.. your second reply has reduced the issue to just one computer.. logically the issue is not the TC.. it is that computer. Ironically I have found logic for computer troubleshooting falls well behind voodoo. 

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