Transcode-0.6.14 has a bug whereby when the '--export_prof' option decides to auto --pre_clip, it switches to the pal profile's resolution, regardless of whether the ntsc profile is selected or not.
Created attachment 47408 [details, diff] transcode-0.6.14-profiles_fix.diff
Please try with 1.0.0_beta3 and if the problem isn't fixed, report this upstream before.
Try 1.0.2, if it's still an issue, report upstream and reopen here.