I've not noticed this problem in CS4 yet but it is occurring frequently in CS3.
It seems to happen most with documents that have footnotes in them. It appears that InDesign sometimes struggles to calculate all the things that are happening on a page. For example, a 300 page document that I'm (or colleagues) are working on is proofed on a printer and then the document saved. The customer will see the pages as they appear in the proofs.
When the document is opened again at a later date some of the paragraphs hyphenate differently which can cause text reflow. It only appears to hyphenate a bit differently here or there.
We need the pages to look like the proofs and so just a few paragraphs running differently to the proofs is worrying, and time consuming to spot.
We've found a quick solution but it doesn't solve everything (most things) – highlight all the text in the document and cut and then paste it back in. InDesign has to rebuild the pages and it runs much more like the original when it was first printed although not exactly.
Anybody know what is causing this? Hope you can understand what I'm saying here!