Hi,

Are there any other programs other than encoder and after effects (non adobe programs) where I can import a premiere sequence and export the final video from there?

I order to have access to a sequence you need to have Premiere open.
You can frameserve to other encoders such as TMPGenc.

After I've tried playing the video on several players as well as on my cellphone and on my tv to no avail, I ended up downloading Premiere 2017. Once I imported the project into 2017 it WAS out of sync....it's just crazy that in premiere 2016 the video was in perfect sync.

What is your source material?

Sorry, maybe I was not clear...after installing Premiere 2017 everything is perfect.