I actually have a slightly similar issue to that. When I select a word and ctrl-F, I get the find dialogue with the word in it. Great!
But if I want to change my search term, if I just click away from the search box (leaving it open in the background), select a new word, and ctrl-F again.... then the search box comes back, but with the old word highlighted. Its a bit annoying. I've gotten into the habit of hitting esc to close the find dialogue before ctrl-F-ing a new word. This way, geany picks up my new word on a fresh ctrl-F.
Its a minor inconvenience, but nonetheless
I can replicate it all day on 1.36
I just tried to replicate it on 1.38..... but worse!!!! If I try to click away from the search box, its forever, ever more, ever, GONE. I can't get it back. Ctrl-F-again "greys out" geany, as if another program has focus, but theres no search box. I can actually see it disappear when I hit ctrl-F the second time (its not "behind" geany or anything). The only way to get it back, is to ctrl-F several times to give keyboard focus to this "phantom" search box, and hit escape to close it out. Then, a ctrl-F will bring it back...... once..... until the cycle repeats!