I've run into this same problem, and the three most common reasons are:
(1) Objects were re-sized with the scale tool, and this actually allows you to create objects with fractional pixel measurements and coordinates, so although the objects LOOK like they are adjacent, the actually overlap by some small fractional pixel amount. Sometimes you can see this overlap if you zoom in very close, select one object, then pass your mouse over the other and look at the corner nodes - if they do not line up exactly, you may have objects that overlap by fractional pixels. (You can also install Aaron Beall's FWAPI Inspector extension - this is a panel that allows you to see the size and position of selected objects with great precision - if the size and position are not integers, that may be the problem.) The fix is to get the objects to have whole number (integer) sizes and positions - you can edit the precise size in the PI or through the FWAPI Inspector panel or by re-drawing the object (and avoiding the scale tool!)
(2) Text blocks are treated like rectangles and other objects, but we don't always notice if a text box overlaps boundaries with an underlying object. Select your text objects and see if they overlap anything.
(3) Nested objects (i.e., rectangles inside rectangles) might be overlapping edges from the inside (in #1 above the problem is adjacent objects overlapping) - this is like #1, except the one object is inside the other but at least one edge sneaks OUTSIDE the outer rectangle's edge.
Since you are using a Master Page, remember to check that objects on a regular page are not overlapping with objects on the Master Page.
I haven't had a chance to look at your file, but if I get time I'll take a peak and see if I can find anything.
I just took a look at your file, and I'm afraid I may not be much help. The two objects that Fireworks claims are overlapping are the header object in the div layer and the media slice in the web layer. Both of these objects are on the Master Page.
The weird thing is that CSS export from the Master Page works - it does not claim that they overlap - but CSS export from another page throws the "overlapping boundaries" message and the export gets screwed up. The two object are clearly 217 px apart, so they are not even adjacent!
Since the Master Page exports normally and the other pages do not, the problem might be in how the Master Page layers are shared with other pages (just a guess...) or something about the layout (slices and objects) on the other pages is causing the problem. I've encountered situations where the exported page layout is totally screwed up in the HTML/CSS, but the problem is not actually where the layout breaks - the problem can also be elsewhere on the page and the screwed up layout is a strange side-effect. For example, just the other day I had page layout in the export actually swap the horizontal position of two sections and a footer that was really messed up. I could NOT figure out why the two side-by-side sections swapped position, so I turned my attention to the footer to correct it. When I fixed the footer problem, the two swapped sections swapped back and fixed themselves. I have absolutely no idea why or how a footer layout problem affected the layout higher up on the page, but I learned that sometimes the problem in the export is not where you think it is.
Sorry I can't be more helpful this evening. If I think of any other possible explanations or fixes, I'll post an update.
Thank you Dave for trying and taking a look at the file. I will continue to review the project and see if there are any other errors that may be contributing to this issue like you suggested.