A quick look shows several inconsistencies:

Check you preference settings for new levels because the Roof Generator generates a level 'Roof-gen' with elevation 365. If you have that set in your preferences (wall-height+floor-thickness=365) than that is the cause. (Dorin can determine if it's because you have a level height of 1 on level 0 that could cause the Roof Generator to use a default.)

Your level 0 is 1 high, should be 300 with walls 300 high.

Change the Roof-gen level elevation to 300 and the probem is fixed. (double click on the level tab.)

@Hans: good find, I missed the different wall heights.