On the mail module, keyboard shortcuts aren't usable anymore when you use the search box. For example, if I search for a specific string in the subject, then, I select a mail (so the focus should now be in the mail list panel), then try to select all with ctrl+a, instead of selecting all the mails which match the search, it's the search string which is selected. Same thing happens if you want to delete mails with the suppr key: the search string is deleted, not the selected mails.

I havent checked if Calendars and Contacts are also affected.