I'm in the process of working on a project using CS5. I'm going back through to make changes to the text. I use text frames for Lesson Headers, Sub-Headers, etc., so each can have its own style. The bulk of the text flows around those header text frames. As I move through the pages to make changes, the text in the frames disappears. Sometimes, the header text frames disappear and I'm left with a blank page. The frame appears if I right click and choose: select/first object above, but the text is still missing.
I know it's there because I've done nothing to remove it. And, I have a print-out of the text in front of me so I know it was there the last time I opened the document.
It sounds like you have text wrap applied to something else on the page and it's affecting the header frames.
But you asked for other ideas, so I'm going to ask what there is about these headers that requires them to be in a separate frame? You can have styles for headers in the main text flow, and you can probably even have a colored background or an image if that's what you need. Flowing text is MUCH easier to control.
Why don't you show us a screen capture of a page so we can see what you are doing? Use the camera icon on the web page to embed the image in a post: