This program has a very responsive, minimal feel that I am really enjoying. One minor problem that I've found is that (on Linux) you cannot copy text out of HTML notepad's default view.
Sciter definitely puts text in GTK clipboard. And it works as far as I can tell, proof: https://sciter.com/linuxnotepad/ on my Linux Mint. So your problem needs some details.
And try recent version from GitGub: https://github.com/c-smile/sciter-sdk/tree/master/bin.lnx/x6...
You will need 2 files from there: html-notepad and libsciter-gtk.so