InCopy and InDesign files viewing differently

I am currently running a project to change a magazine publisher from a Quark platform to an InDesign and InCopy workflow. One problem that keeps occuring is that when an editor manually alters the paragraph style to make the copy fit in InCopy, (ie, altering the tracking and/or leading), this change does not show when the same file is opened in InDesign.
For example, a heading that an editor has reduced tracking -5% to make fit into one line in the InCopy file, will still look like two lines when the InDesign file is opened. This is particularly dangerous for pages of text, as we keep losing lines from the bottom of the page and this can be easy to miss during output for press.
I've checked, and all staff are following workflow, and updating assignments - so it's not human error (as far as I can see).
Is this happening to anyone else? And is there a fix for it? The only one I can think of is to add more paragraph styles with different trackings etc, but this is not ideal and does not cover all the variables.
We are using CS4, and the Snow Leopard platform – Please help!

As an update to this, I have found what I believe is the cause, and, hopefully a fix, to this problem.
The cause seems to be that in the original Quark template, the font has a horizontal scale setting of 95%. When the template is converted to InDesign, everything looks fine. However, the font doesn't seem to be recognised as a true font, and this has resulted in the word and character spacing looking completely different between InCopy and InDesign. This has been causing problems such as;
1. Headings showing in one line in InCopy but flowing onto two lines in the InDesign file
2. Body text showing completely different spacing throughout - causing uneven window and orphans and resulting in paragraphs being in different places in the InDesign and the InCopy files. This has made it impossible for the editors to fit copy on page.
Note that any written changes by the editor (ie, change to the words) has worked fine.
The fix seems to be to go back to the original template in Quark, and make sure all the font/text settings in the paragraph and character styles are set at 100%. Then make the template conversion again. I have run some testing this afternoon, and everything seems to be running ok now - touch wood!
Thought I'd send an update anyway in case anyone has the same problem.

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