Something along these lines are the likely cause as all the titles are fine when playing from another country where they are natively on D+, its only the Hulu versions that experience this. It becomes most noticeable on longer titles such as the Macross Plus Movie Edition where subtitles are appearing upwards of 7 seconds too early near the end. Checked the Frontier and Delta movies however and they seem fine, just something they need to fix on a few titles then.
I did spend a long chat with Hulu support reporting the issue on Plus Movie so maybe it'll get fixed one day.
Also made sure to send requests for improvement on both Hulu and Disney Plus requesting they add non-CC versions of the subtitles for all titles.