I don't know that I have any solution; something just doesn't add up, and I'm trying to understand.
But the sample you provide uses colons, which is incorrect for drop frame timecode.
This suggests you created nondrop frame timecode for the subtitles, instead of dropframe.
DVD for NTSC is dropframe. But I just did a test, and Encore appears to accept the colon type file, but places it after converting it as nondropframe.
A feature request would be for Encore to warn you that your are importing a script file that does not match the project setting.