In the separate message window, only the shortcuts that are defined in the windows' local menu are available after the window is opened. To make other shortcuts work (most notably DELETE for moving current message to trash), the text area needs to be focused by clicking on it or hitting TAB once. This behaviour should be changed to make *all* shortcuts available from the moment the window is opened. An obvious solution would be to add all the relevant items to the menu of this window - the edit menu is currently missing items for deleting the current mail, for example.
Changes related to this bug have been committed. Please check latest CVS and update the bug accordingly. You can also get the patch from: http://www.claws-mail.org/tracker/ 2012-11-12 [colin] 3.8.1cvs118 * src/messageview.c Fix initial focus on textview. Fixes bug #2776, "Make all menu shortcuts work properly in the message window"