Comment 1 for bug 1647767

A fix went into the head of the gtk3 branch for fixing the scrollbars reappearing, *after* 1.90 was released.

I can't replicate the transparency not being persisted. It works for me. It's possible that something is going wrong on startup that is specific to your combination of system, libraries, and config. Can you recheck with the head of gtk3?

Also to be sure, can you check you ~/.config/terminator/config file after you exit, that it contains lines something like:
    background_darkness = 0.88
    background_type = transparent
in the profile that you are trying to reopen with.

https://code.launchpad.net/~gnome-terminator/terminator/gtk3