Try snapping them to grid. Don’t know if it happens in ET, but in Medal of Honor mapping non-cubic brushes tend to randomly disappear if you don’t snap them to grid.
Brush faces disappearing after compile
d11
(d@Ve)
#22
they was snapped to grid…but i figure out why they was disappearin tho…i have 2 brushes 214units long, 4 units thick, and 10 units tall. but i had a 1 unit slant in the length to match up the ajoinin brushes…now that ive got it figured out i have alot of mapping to fix lol…it seams i mess with somethin for hours tryin to fix it and soon as i post in this forum…5 minutes later i figure it out…makes no sence to me
ill have another problem soon enuff 
im sure of it lol
thankz,
d@Ve