Starting AWB logged in under an alternative account, when the browser is logged in under a main account and message is posted to the alternative's talk page, the "You have new messages" prompt is not cleared when the alternative's talk page pops up, and no further editing is allowed. Workaround is to log in using the alternative account in an incognito tab (or another browser) and read the talk page, which of course is not hard.
A proposed fix: add a public method, say "ClearHasMsg" to WikiFunctions\API\ApiEdit.cs containing the call:
HttpPost(new Dictionary<string, string> { { "action", "clearhasmsg" } }, new Dictionary<string, string>());
and call TheSession.Editor.SynchronousEditor.ClearHasMsg() in WeHaveNewMessages(), immediately after displaying the talk page.
I don't believe this will introduce any regressions, because by virtue of displaying the talk page the flag will be cleared anyway for non-alternative users.
I acknowledge this is the lowest of priorities, as I may be one of very few (or no other) editors using an alternative account, and it rarely gets messages. But it seems to also affect bots, and would be an easy solution to T347252.