I somewhat found the answer. I was converting the .tiVo files to .M4v before I was burning them because I was putting some on my iPod as well as archiving to DVD, I should have just left them as .tiVo files.
Now when I try to burn a .TiVo file an alert tells me something like "Popcorn is set to burn the DVD as PAL and it will need to convert the .TiVo file to PAL 1st. Do you want to convert file or burn as NTSC?" Then I can tell it to burn as NTSC.
Problem is I don't get this alert from other video sources and those still burn as PAL. But the main reason I got Popcorn was to use it with my TiVo.
Roxio/Sonic Solutions support was no help they e-mailed me back once with another question, I clarified my problem and asked if it was possible they sold me the European version by mistake, they never wrote back.
I never found a way to set the preferences to NTSC.