Difficulty exporting InDesign file to PDF

I am an InDesign newbie, using CS4 on a Mac. I have inherited a 16-pg InDesign document that was created by a graphic designer from his home (also using a Mac); he is no longer with our company and is not available for advice. We are trying to replace fonts he used in the document, plus some links are missing. The designer turned over most of his files before leaving but did not package the documents.
The problem: There are several instances in the document where a layered graphic element (with text on top) overprints when the file is exported to PDF, covering the copy. (I've tried all variants of PDF - from high quality to small - and it does it every time). When I check the file in InDesign, it looks OK, until I click the Overprint Preview command; then I see the way the image bleeds over onto the text, but I don't know how to tell it not to do this! I'm new to InDesign and am not sure how to change settings for elements. I have tried to click on this layered element to select it & find out its attributes and properties, but nothing happens when I click. I have been able to change the font for the top text layer, but that doesn't make any difference in the PDF export problem.
The designer created another 16-pg document similar to the one with the problem in it, using a very similar graphic element. (These docs are two versions of a sales kit -- one with prices, one without.) For some reason, this document does NOT overprint when exported to PDF. So far, I haven't been able to figure out what settings are different in this document.
I don't know if the layered image was created in Illustrator, which the designer used to create some of his graphics. I do have access to Illustrator and also am attempting to learn this program so possibly could make some fixes if need be. I have Photoshop but not Acrobat.
Thanks for any help!
Lorna

I don't fully understand your problem but I'd like to help.
By Shift-Command-Click, I think you are referring to selecting underlying objects. I'm on a mac, for me it's command control click. At any rate it's not related to locked objects, it's a method of selecting an object when other objects are stacked on top.
Possibly your text is on a locked layer. Window: Layers - check to see if any of your layers have a padlock icon.
Also it could be on a master page. View: Show Frame Edges. Master page elements will have dotted outlines, they can be edited on the master page.
Regarding images - there are two possible selections to make. One is the container, the other is the content. To select one or the other, Object: Select: Container or Content. There are also little icons in the control bar that allow you to do this.
With containers, you can select the bounding box, or you can manipulate the anchors. If you select the object with the Selection Tool (dark arrow) you get the bounding box. If you then switch to the Direct Selection tool (hollow point) you can change the anchor points. To be clear - if you select the box with the direct selection tool to start with, you will select the contents (if there are any), not the container.
With InDesign, a container object is one of 4 things - a text box, a graphic box, an unassigned box, or a mask for other containers. Sometimes it is hard to tell what you have. Learn to distinguish text boxes from other types by looking for the small white boxes in upper left and lower right when you select them.

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