I have created several ellipses using Inkscape. I can select multiple ellipses, resize them together, and then save the file as a PDF. When I do this, the image is not rendered the way I want it to be rendered in the PDF viewer. When I reduce the width of the group of ellipses(actually arcs, like at McDonalds), the PDF shows ellipses that are thicker at on the tops than they are at the bases. I want my ellipses to have the same thickness at all points. Is there a way that I can get around this problem?

I don't know enough about PDFs to be sure. But one thing you can check in Inkscape is in the toolbar for the Selector tool . Usually all the way to the right of the toolbar is a setting for "Scale stroke width". If it is checked, then your stroke width scales when the overall object is scaled.

But again, I don't know how saving as PDF might affect this. And surely other members will reply on that point.

It's a bug in 0.46 version and I get the same behavior as you do, variable stroke width of the arc.

PDF export has been greatly improved since the official 0.46 version and in the current development version I can no longer reproduce this bug so it's safe to say it's been fixed.

If you can't wait for the official 0.47 version try downloading the development version, you can have both official 0.46 and dev build installed at the same time.