I have one of the weirdest glitches I've seen. I've been using Premiere for years and have always found an answer somewhere, but this may be a new one.
I have a commercial for a client that I'm working on. It's fast paced and transitions are used everywhere. We use custom made transitions on adjustment layers for this client, and have been doing so for about a year.
I'm running into a weird thing where the transition is populating on the program monitor and rendering in Premiere, but isn't showing up in the final export. It just cuts from one clip to the next.
But, of the 6 transitions in the timeline, only 2 are not working. The other 4 are fine.
I've updated Premiere, uninstalled and reinstalled, copied the sequence, changed sequence settings, changed export settings, duplicated the sequence, copied the files manually from one sequence to the next, turned my computer on and off again, and of course, checked to make sure the layers are not hidden.
to summarize, in your sequence settings, set your preview format to a high quality codec (best to match your output format), render your entire timeline and then when you export make sure "use previews" is enabled.