Deep Clean with InDesign Interchange Format (.inx)
New InDesign users may know that exporting an ID CS2 layout to the InDesign Interchange format is how CS2 files are "saved back" to CS1 (the CS1 user can open the .inx file and it'll be converted to an InDesign CS1 .indd file, sans CS2-only features of course).
They may not know what grizzled InDesign vets already know, that the .inx format is great for repairing the occasional flaky, bizarre-acting InDesign document, even if it's never opened by anyone else but the same user who exported it.
It's easy to do. With the CS1 or CS2 layout file open (this troubleshooting method works with either version), choose File > Export. In the Format drop-down menu at the bottom of the Export dialog box, choose InDesign Interchange, which changes the filename extension to .inx. Save the file, then open the .inx file right up again in the same version of InDesign you used to export it.
It opens as an Untitled .indd document; looking exactly the same as before, all colors, links, page items intact, but (usually) free of any random internal cruftiness that may have prevented you from deleting an "I'm positive it's not used" spot color or other such oddities. To continue, just save the document as a regular .indd layout file with a new name (or the same name as the old one, replacing it) and go on your way.
If the export-to-inx routine didn't solve your problem, there are other things to try, but do this routine first.