To clarify -- when you say "... if you click each account the emails will then appear in the messages pane." -- what type of click? Are you double-left clicking on the account? (which would display that specific accounts messages) or doing some other type of click? (One left-click so that the account is merely selected should have no impact of any kind on the In-Box display based on defaults).
When you say "... is to reboot PP." -- is that to say you are stopping and re-starting PP (stopping/starting the process) or are you rebooting your computer? (my impression from your "... shut the program down and restart it." comment is that you are stopping and restarting PP by specifically "exiting" PP (via the PP "Exit" option) and then restarting PP.
Questions:
1) What do you have for this "View" setting (when this issue occurs)?:

- If this setting is not "All Accounts" you could be displaying an account w/out any messages in the In-Box
- All Accounts.png (6.57 KiB) Viewed 2209 times
2) What do you have for this "Junk View" setting (when this issue occurs)?:

- You want to make sure you are not filtering valid messages out of you In-Box
- Junk View setting.png (6.08 KiB) Viewed 2209 times
3) What do you have entered in the "
Ini location" and "
Data path" values in PP's "
Storage" window (go to "
Tools" > "
Options" > "
Storage" window from the
main PP menu to get to settings)? Problems can arise when a path starts out with "C:\Program files..." due to Windows UAC which can result in Windows preventing POP Peeper from saving settings and/or data as of the time that POP Peeper is exited or Windows is closed. If this is the case then please get back to us (based on your explanation this does not appear to be the case however).
4) What version of PP are you using (Help>About POP Peeper...)?
5) What computer Operating System are you using?
6) What type of account(s)? (i.e. Gmail, Yahoo etc.)?
7) When this happens -- (assuming first 3 questions are not relevant) have you tried from the main menu "Messages" options doing an Uncheck of the "Enable Display Filters..." option to see if messages then appear in the In-Box pane? (Important Note: this is a temporary setting only for testing and should be returned to a "checked" [enabled] status).