Okay, two things to try.
Nest the sequence in a SD ProRes anamorphic (make sure it is 720×480 and not 486) framerate needs to stay 23.98, and field to NONE. Then try the export and compressor or send to compressor.
or
Take the HD QT and in compressor turn on Frame Control and set to best. You can set In and Out to just do a sample of the problem area. This is a long encode, I would test with CBR then if you get good titles and want to go back to VBR you can do it overnight.
The pulsating is something I don’t know about. Closed GOP should have nothing to do with that. I assuming you have not changed the GOP structure.
Let’s see if any of that helps and we will go from there.
Also how are you viewing the encodes?