What do you mean when you say "nest my pages"?

Anyhow, I am seeing lots of "not found" files in this list -

But I don't see a reason for the missing images to be sized differently as they are....

It means that the links that are contained in your pages do not point to the correct location on the remote server.

The first rule of working with files in DW is that you NEVER move files around using FINDER/EXPLORER.  If you move files, move them from within the DW Files panel.  That will keep all of your files properly linked.

Next, to achieve your "nesting" (which is normally how sites are organized), just create the folders in the site using DW, and place the files you want to be there within those folders.  For example, if you want to have a link like "resources/communication_manuals.php", you would create a 'resources' folder in the local site at the root level, and move the 'communication_manuals.php' file into that folder.

Make sense?

This page - http://www.foxthermalinstruments.com/ - is at the root level of your site.  It links to the arrow image you use in your left menu like this -

<img src="horiz-menu.css3prj_files/css3menu1/resultset_next.png" alt="Applications">

This page - http://www.foxthermalinstruments.com/ft3/ft3.php - is one folder level below the root of your site.  It links to the arrow image like this -

<img src="horiz-menu.css3prj_files/css3menu1/resultset_next.png" alt="Applications">

That's clearly wrong as it should be like this -

<img src="../horiz-menu.css3prj_files/css3menu1/resultset_next.png" alt="Applications">

Does the left navigation on those pages look right when you open them in DW?  Have you moved the pages to other folders when you upload them, or are they uploaded to the same locations on the remote server?

Anyhow, the solution is to just remake the links in DW so that they point to the correct locations.