After using a 2nd monitor with my notebook, claws mail will place its main window on the secand montior even if this monitor has been disconnected. Problem continues even after reboot.
I presume that the mainwin_x is out of boundaries if your second screen was "to the right" of the main one and is now off. As a workaround, unless using other window handling tools at window manager level (devilspie or other), you could close CM (from the command-line --quit or kill it), edit ~/.claws-mail/clawrc to reset the mainwin_x value to 0 and start CM again.
*** This bug has been marked as a duplicate of bug 4718 ***