This is probably a very easy problem to solve, but I've tried a few things with no luck...
When saving to pdf, the program doesn't "do" my transparencies, and it brings to front objects that are placed below others.

Trying to save as postscript and then convert to pdf didn't work for me, becuase ps also doesn't support transparencies.

I need a pdf file though...any suggestions for seasoned users on how to save a pdf true?

Many thanks,
Shannon

have you tried selecting the objects and using the make bitmap copy option. This will add a bit map in your document instead of the vectors and then save the pdf with inkscape. Its just an idea and maybe not exactly what you inteded.