Try restarting DSiMenu++ and see if it still looks like that (after setting the theme). I think it's just a visual bug that happens sometimes. I get it in games every now and then.
No i have delete the folder for DSimenu++ fully and nothing is always the same, but i can tell you i don't get it on games.
I have fix it,well i think...mot sure
I have remove 2 files from the latest version and replace them with the ones in the older version
the files are from the dsimenuplusplus folder :nightly-bootstrap and release-bootstrap and use those
from the 5.4.1 version this fix the 3ds theme and the other themes as well. i still have v5.5.1 in settings.
and everything is working, not sure if i found a fix or i mess it up or delete a file that contains something
important not sure i just know that is working, is working with fowarder too
