Thank you for your answer,
All those pdf's are made from scratch using DynamicPDF, but aren't made all at once. The resulting pdf's are merged together at a later time by finding the various files on the disk, so those performance considerations, while useful, don't really solve my problem.
From what I found out, the merged pdf contains multiple copies of the Verdana font, and when I use the save as functionality of Acrobat it merges those fonts together so there is only one. This can be seen by looking at File->Properties, on the Fonts tab in Adobe Acrobat.