There are couple of possibilities here:
1. You have a situation with too many Vusers with each Vu throwing hundreds of error messages onto the output window. Solution: If you have used lr_error_message function in your script, then try to minimize the usage of it. Plus, you can also ensure that your script throws minimal errors by incorporating correlation and content checks.
2. You are using an older version of LR (9.0 or 8.1 or older) The older version had problems with dockable output window settings. If you have accidentally placed the window in a negative co-ordinate(outside the context of controller window) then your OUTPUT_FRAME_PLACE parameter in wlrun7.ini(drive:hp/loadrunner/config/) would be set with a negative value, which means your output window should technically fall outside the controller window and hence the problem.(Solution: Restart controller and reset your to output_frame parameter to a safe value. eg: OUTPUT_FRAME_PLACE=63,254,955,616,)
3. Your output window is docked and/or miniaturized or placed in a corner and you are overlooking it. Solution: Find it and expand it ;). I have seen many people goofing up because of this.
-Chaitanya M Bhatt
http://www.performancecompetence.com