(I'm running Pegasus Mail Version 4.70 (Win32), Feb 27 2014, build 546, on Windows 8.1)
I've noticed this gradually over the last few months - I'll send an email, and select a folder for my local copy; but when I open that folder I can't find the outgoing message. Oddly, if I search for the message, it will be found. I'm not sure this happens all of the time; usually I'm in the midst of work, and only notice when I need to go find a copy of a previously sent message. It may happen all the time, or may happen only with certain folders.
I've searched the fora for similar reported problems - it seems something like this may have cropped up before, but I don't recall there being a clear solution. One suggestion was to rebuild the hierarch.pm file; but I have a fairly substantial structure in place, and it would be a major pain to document it and rebuild it. Especially if this has to happen periodically; maybe there is some programmatic way I could do that, so it would be easy to repeat.
I do have two mailboxes on my system; my main one in C:\PMAIL\whatever, as admin, and an archive one on a larger drive. I'm the only user.
I don't know if it's related, but in some of the folders where this happens, the default sort order changes back to alphabetical by sender, no matter how I choose to view the folder. (I thought it was a global setting to preserve the last view (sort order) - that works on most of my folders).