When I went to clear the three alerts from a PM conversation yesterday, each page I clicked led to a 404 instead of leading me to the PM conversation. It's not a problem in terms of usability for me since I didn't use the alerts to look at the PM conversation, it's just odd.
Thank you for reporting this! Yea that's definitely odd.
I installed a development plugin recently that completely overhauled the private messaging system. It's actually a beta plugin, so there are things the author is still fixing here and there. However, it's a plugin that we paid for, so I have no doubts that the author will eventually address them with time.
I'll report this. Thanks for letting us know!