Did the user have 2 monitors in use at one time? Usually that is the issue, the coordinates for the manual runner window are mapped to real estate that can't be seen without that second monitor.
Some fix options for you:
1. Right click on the manual runner in the task-bar and choose MOVE. Next click on the keyboard arrows to lock the window to the mouse. By moving the mouse, should be able to move the window hopefully over to your main display window via mouse or keyboard key movements. This can be tricky, and you may get it work easy or you may not.
2. Could attempt to rewrite the DB values for the coordinates for the manual runner window with values from another user who does not have the issue. There is some sql code out there to identify the coordinates, but that is little involved and require some sql knowledge. Easier and quicker step would be to just remove the user from the project and then re-add them back, which would default reset the user's values. Such would remove any user favorites or settings like that, but user can add any such things back. If the user balks at such, if they have a lot personal preferences, then try the coordinate code directly which is below.
Here is some sample code to do the coordinate change from one working user to replace for the user with issue.
Option 1:
Replaces coordinates from a user 2 who is working fine and writes over user 1 settings who have the issue.
update common_settings
set cset_value = (select cset_value from common_settings where cset_owner = 'User2' and cset_category = 'MunRunsFormFrm' and cset_name = 'frm_man_run')
where cset_owner = 'User1'
and cset_category = 'MunRunsFormFrm'
and cset_name = 'frm_man_run'
update common_settings
set cset_value = (select cset_value from common_settings where cset_owner = 'User2' and cset_category = 'TestInstancesFrm' and cset_name = 'frm_man_run')
where cset_owner = 'User1'
and cset_category = 'TestInstancesFrm'
and cset_name = 'frm_man_run'
Option 2:
Deletes the saved coordinates for user 1 with issue and forces QC to create new entries with default values.
delete from common_settings
where cset_owner = 'User1'
and cset_category = 'MunRunsFormFrm'
and cset_name = 'frm_man_run'
delete from common_settings
where cset_owner = 'User1'
and cset_category = 'TestInstancesFrm'
and cset_name = 'frm_man_run'