I've been using Pegasus for years - very happy with it! Only "flaw" is maybe forwarding HTML emails from others, usually "commercial" - formats get lost.
Most "commercial" messages are very poorly formed. They abuse HTML and CSS codes and note rarely use scripts which are forbidden in Pegasus Mail for security reasons. In those cases forward them as attachments and your recipient will get it entirely.
Current issue: all of a sudden - today - one incoming email to one of my four email addresses seems stuck somewhere - it keeps downloading /new mail every few minutes. Never happened before.
I shut down and rebooted. With that address open every few minutes I get the "new mail" notification, and the same email comes in, again and again.
Win 7, Pegasus 4.73. No recent changes made. My other "main" address seems just fine - normal.
You said you have it sorted but you could have also mentioned your mail provider along with your Windows and Pegasus Mail versions. Certain providers behave differently over POP3 (I'm assuming here) commands. To exemplify, a typical retrieve and delete a downloaded message translates as...
- Gmail - Download message, mark it as read, and move it to account's archive (depending on settings it may be changed).
- Yahoo! - Download message and move it to account's waste bin.
- GMX - Download message, mark it as read, and leave it on account's root directory.