Font issue with InDesign and OS 10.6

I have read quite a bit on this but have found no resolution. We installed OS 10.6 on two of our three G5 Macs at work. We use InDesign CS4 and OS 10.6.5.
When we open an InDesign file that we all share, the machines with 10.6 on it say fonts are missing. (I believe this is a naming convention problem.) I learned that some of the fonts for InDesign should be moved to the InDesign font folder. We did that. That helped on several of the fonts. However, we still have an issue with Helvetica Neue, and Universe (67 or other numbers). I have the same Universe font family listed, but when I go to find 67 or 47, they aren't there.
Anyone else having this problem? Do we need to go in to every document and change the fonts to avoid this error? Is there a better fix?

I have just swapped from an old Mac Mini (using 10.4.11) to the new Mac Mini (using 10.6.6). I did not do any fiddling about fonts. Everything is as it installs. The only thing I did is to resolve duplicate fonts in Font Book.
For convenience, I used Arial for documents. Now when I open an ID document, it says Arial[TT] (as well as bold, italic...) is missing. I checked the Arial ttf group is in /Library/Fonts, but in ID font list, it shows an Open type.
All I want is that the fonts should work, when I open all the InDesign documents (still in CS2 Version) that I created since last five years. I am no techie by any means, what I need is a step-to-step to solve the font issue, so that I can get on work immediately.
Any concrete step-to-step advice is highly appreciated.

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Thanks for the info. As you said, if this is happening when you have only manually activated fonts, then the auto-activation isn't coming into play which does lead me to think it is related to the plug-in generally and maybe the sleep issue, which you say you definitely have. So I've added you to the sleep issue tracking.
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6)      Click the "Save" button again and save the file to your desktop.
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Uploaded with plasq's Skitch!
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Uploaded with plasq's Skitch!
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Font issue with InDesign and OS 10.6

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