I had the same problem. My problem turned out to be two different issues. 1) I use Outlook from my home computer. When Outlook gets the email, it is configured to remove the email from the server. So my Pre would get the header, but the email was actually gone before I ever tried to read it. I have not configured Outlook to leave the email there for 3 days. The same thing would happen if you had your email client setup to move the email to a different folder. 2) I also use a program called MailWasher that is to catch and remove spam. It runs every x minutes and moves suspected emails to a special folder. So my Pre would get the header, but the email was actually gone before I ever tried to read it. This could be going on with your gmail, hotmail, or other email account that supports spam filtering.
I have the same problem and have tried to post it and get help in several forums. My company email comes through gmail -- Google apps. I think that may be part of the problem. But at the moment, I can't use the Pre email program because I lose most of my email before I can read it. I'm using Snappermail through the Classic program, but that has other limitations and problems. I hope Palm notices these reports and fixes the issue.