These are files that are very small, but turn and load very slowly. One way around this is to resample the images at 150dpi so they turn and load faster in the iPad. Here is a method using colorsync on the Macintosh.
also for Lion:
Using colorsync to resample the images at 150dpi can produce a larger file (less compression), but can make the file much faster at loading and turning pages.
Here is a Windows version which seems to offer the same type of functionality (have not tried this one)
Create an Automator Workflow
Include Ask For Finder Items
Copy Finder Items
Apply Quartz Filter to PDF Documents
(Note: you must make a copy of the filter before you can change settings)
Set Resolution to 144
Max set to 1024
Set Image Compression to:
Quality center - right in the middle