Apparently WinCompose (great program, by the way :) ) has problems with Gtk3 applications.
In CherryTree ( https://www.giuspen.com/cherrytree/ ) instead of inserting a special character, WinCompose inserts code of the character (or characters). For example:
using ~~ instead of special character: "≈" a code value of this char appears: "2248"

I've opened an issue for CherryTree (see: giuspen/cherrytree#1341 ) and investigation revealed, that problem is with WinCompose and Gtk3. Another Gtk3 application, Inkscape, also behaves strangely.