Thank you so much for your reply!
I actually just figured out the problem. It was caused by having some calls to ggplot() that did not have any geoms associated with them because the data were missing (these reports are run dynamically while drawing from a sql database). The empty plots were for some reason being saved as png files in the "files" folder. The reports looked fine because those plots were empty as expected when there was not data, but the png files were being created for some reason and that overrode the "self contained" call.
So... I wrote some IF statements to only draw the plot if there is actually data and that seemed to solve the problem.
I can still send an example if you want, but I think the problem is solved so I wouldn't want to further waste your time!
Thanks... Leslie