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As I recall, demerphq implemented several bits of persistence for Message Inbox options. That would be my guess as to what is causing you problems. The link with srch_folder=0 should (and does appear to) reset most of these options for that visit.
But my attempts to narrow down the cause just eliminated all persisted options. But that probably just means I missed something.
You have an inbox-related setting with a value of "From". I'd expect that to cause the "From" checkbox to be checked and the "To" checkbox to be cleared which would cause the page to display the messages from the adjacently displayed inbox owner (you) instead of those to you.
But there are also several contraindications against that cause. If "From" is checked, then the number after "Inbox" would be the number of messages from as well. Further, having the "From" checkbox be the default should be ignored when you use the srch_folder=0 link (but maybe that wasn't (properly) implemented). I did not succeed in making that option persistent for me, but I only tried the obvious.
The observed behavior might be explained by a persisted "offset" into the list of messages. But I would hope that that value could not be persisted. If it were, that would be discernible at the bottom of the (empty) list. I also saw no such persisted option in your options (and they are listed alphabetically and their names are prefixed such that related options are listed together).
There are also options for which direction to sort messages and at which end to truncate the list. It certainly could be a bug in a particular combination of those options. (I recall at least some confusion involved in some code updates related to those.)
A solution is likely to be found either in one of the form elements on the Message Inbox page or in one of the overly numerous form elements on User Settings or one of the other settings pages linked at the top of it.
Perhaps one of the dozens of pmdev members might follow up if that isn't enough for you to be able to find a solution or if, after finding the solution, you believe this is actually due to a bug that should be fixed.
In reply to Re: "Message Inbox" is not displaying messages (options)