I thought I'm gonna resurrect the thread, as I have similar problem.
I have an LCD module (standard 16x6 character LCD) which has a row of pins in top left corner, 4 mounting posts, but other than that there is ~10mm clearance underneath. I have defined area for the LCD as "keepout" and "higher than 6mm". It seems to work as long, as smd parts underneath don't have any area defined. I have defined an area with body clearance checked and body height set at 2mm, but I still get errors.
How do I define areas for those two parts correctly to get rid of the errors?
Create an area that is just encompasing the actual pins for the LCD and define that as the body area. Create an area just larger than that you've just created for body area for the pins and define that as your placement area - for the clearance you require around the pins. Create a new area for the rest of the LCD, set up the component keep out if higher than for this area, and don't have it set as a body, nor a placement area.