I've noticed other instances where the auto-suggest does not disappear:
- adding term to glossary with the Alt+Ctrl+G shortcut: the pop-up remain open overlapping the window for adding terms.
- using PgDown to go to the end of the segment (remapped to Cmd+Down)
However, for me the pop-up hides if I insert a non-breaking space with a Ctrl+Shift-Space shortcut, so I do not experience this particular issue.
Overall, I've noticed that I tend to overuse Esc key in CafeTran to hide auto-suggest in different cases. I might pay more attention to when it happens.
I have even remapped Esc to "Ctrl pressed alone" not to reach to it every time.