I'm in a serious problem in which Adobe Media Encoder is outputting the file as variable frame rate. This is unacceptable for most major OTT platforms. Don't know why on some files it would be constant frame rate and others are variable. Could it be the profile and bit rate affect this?
This doesn't sound right. Help us to help you, we don't even have a clue what file type you are outputting or what settings may have been used. Please post a screen shot of the Export Settings panel so we can see what you were doing.
Premiere does not like editing variable frame rate, and I'd be very surprised if it was outputting such a thing