how are you trimming the walls? using the Wall Trimming option is quicker but not as efficient as using solid element operations(SEO's) IMO. select all yuor walls that have been trimmed, open wall settings, cancel the trim operation, open SEO dialogue, with walls selected, hit Get Target Elements. Then deslect the walls, select your roof/s and click Get Operators in the SEO dialogue. Choose the 'extrude upwards' option and apply!