Hi all,
This took me a good long time to track down, and since I didn't find any information here and Adobe technical support was no help, I figured I'd post the result. Happy new year.
Here was the problem. Working in CS5, intermittently we would get font reflow issues. In addition, when going to edit the type boxes with font reflow, we would get the message, "This text was created in a different version of Illustrator. Editing the text may cause some changes to your text layout. Basic formatting will not be affected. Do you want to continue?" Please note it says "different version" rather than "previous version". These files originated and stayed in Ilustrator CS5! If we hit OK, the type would snap back to the original state!!! Worse, if the type was copied and pasted, or anything in character or paragraph styles was edited, it would snap back without ANY warning. Now you see it... now you don't. Major problem in any print environment.
So here is what I found, and this is a CS5 exclusive. If you are working on a file and have a font set open which includes a font from one foundry, and then opened another document and activated a font set with an identical font from a different foundry (the original font closing), the kerning for the original document (in the background now) would be set to zero (rather than auto) and the font would reflow. If you didn't notice the reflow, and saved the file, well it would create the condition as described above. Of course it isn't ideal to have the font foundry change like that, but bottom line usually you could get away with it... maybe with one or two characters moving slightly. In the new CS5 world, Illustrator decides you really don't need ANY kerning pair information and then helpfully tells you it was a "different" version of Illustrator that caused this. Heh.
What a mess. Bottom line, make sure your font management application is set to throw warnings when conflicting fonts are opened, and most importantly, leave the original font open! Do not allow the new font to be opened until the conflict is resolved.
If your font management application does not have this option (Universal Type Server 1 did not), you better upgrade or forget about using Illustrator CS5 in a heavy production environment.
Adobe, this was a major change and a major headache. You have some explaining to do...