There is one thing for now that I can think of to check regarding a Pop Peeper (PP) individual account setting which is to see if this individual account is set to use your default retrieval setting that you have mentioned.
To check this you need to have "Advanced Options" enabled (it is probably already enabled). To be sure this option is enabled, on the PP main menu go to "Tools" > "Options", make sure "General" is selected in the left pane, if "Advanced Options" is not checked (enabled) on the top-right area of the right pane then check this option and click "OK".
Now check the following setting for this individual account:
1) Edit the account (right-click the account and select "Edit")
2) Select the "Advanced" page
3) Now make sure "Default" is selected for the "Retrieval option" setting
4) Click "Update" if the "Retrieval option" needed to be changed
If the above does not apply then another possibility is that the message(s) for this account may possibly be "hidden" in PP.
In the main PP menu bar go to "Messages" and uncheck "Enable display filters" after which you will get a popup window that will explain what this does. Doing this may help display any "missing" messages. You should then check the "Enable display filters" once again to enable this option after you have determined if this was your issue in this case.
Refer to the last two posts in
THIS TOPIC for details regarding the different options you can take to list emails that do not appear in the account(s) inbox.
Please post back if any of this helps you out in either this post or in the linked topic.
Good judgment comes from experience and a lot of that comes from bad judgment. - Will Rogers