After Effects keeps overiding my custom presets on export. It turns projects into tiny size and is inconsistent in this. I can do several projects then After Effects suddenly ignores my preset and turns projects from 1920'x 1080 to 352. I have called several times, trying to get an ad out and now Adobe is closed. I am really ...angry.
Make sure you save your custom preset and give it a name. Make sure the format you choose supports the frame size you need. Your comp frame size should match the output frame size. The frame rate is also dependent on the format you choose. H.264 is very picky about frame size and frame rate. If you are using the render cue you can choose any saved output module template as the default.
Let us know if you have any othe questions. If you are still having problems we need workflow and render details.