I am having a problem with bounding boxes. They seem to be getting bigger as I work on my project.

Some times they are not centered on the object. Here is a screen shot of the problem. Both objects are the same width.

The object on the left has something going on. Can you upload an svg file for us to examine?

There is no problem : your settings (inkscape global preferences > tools) must be to visual bounding box, so the size of the filter area matters for bounding box size. Switch to geometric bounding box for accuracy (be aware that the bounding box doesn't take stroke width into account, then).

Thank you for your reply, That solved the problem.