Had a lot of trouble getting crop and resize to work together. Trying to take 2.39 AR movie, crop in vertical to remove black bars, and crop in horizontal for 16:9 AR, then resize to 1280x720 (e.g. from 1424x800). Tried it 5 different ways before getting it to work.
Had to go to the crop tab, autocrop, switch to manual crop, change the numbers for vertical, such as 0,0,138,138 (804 height) to a mod 16 height such as 0,0,140,140 (800 height). Then take (1920-(800*16/9))/2=248.888, set crop to 248,248,140,140 for resulting size 1424x800 (1424 is also mod 16).
Then on the Resize tab, click the button for Custom size and set to 1424x800 to match the source. Then click the button for Zoom from source, and in the list will be 1280x720 (hopefully!).
I tried this multiple different ways, and each of the first 5 times, it was ignoring the crop and merely resizing the uncropped original 1920x1080 to 1280x720 retaining the black bars.
Each time, the sample in the Resize tab window had looked exactly like what I was shooting for--but that's not what got rendered. The output did not match what I saw in the sample window. Until finally it worked using the recipe above. 
Lots of people post with problem with crop not working, with forum participants having difficulty reproducing the problem. There is definitely bugginess going on in there with respect to cropping. But it can be made to work.
Had to go to the crop tab, autocrop, switch to manual crop, change the numbers for vertical, such as 0,0,138,138 (804 height) to a mod 16 height such as 0,0,140,140 (800 height). Then take (1920-(800*16/9))/2=248.888, set crop to 248,248,140,140 for resulting size 1424x800 (1424 is also mod 16).
Then on the Resize tab, click the button for Custom size and set to 1424x800 to match the source. Then click the button for Zoom from source, and in the list will be 1280x720 (hopefully!).
I tried this multiple different ways, and each of the first 5 times, it was ignoring the crop and merely resizing the uncropped original 1920x1080 to 1280x720 retaining the black bars.
Each time, the sample in the Resize tab window had looked exactly like what I was shooting for--but that's not what got rendered. The output did not match what I saw in the sample window. Until finally it worked using the recipe above. Lots of people post with problem with crop not working, with forum participants having difficulty reproducing the problem. There is definitely bugginess going on in there with respect to cropping. But it can be made to work.