That's pretty accurate. It says "installing theme" and shit but I exit and nothing. I reboot, nothing. I replace the theme on the sd card, same results.
Okay, I got some bad news for you but don't freak out. What you have is a corrupted theme ext data. Those happen either from having too many themes all at once, changing SD cards with 32 KB to 64 KB cluster sizes (vice-versa), or even installing out of region themes different from your 3DS native region. Whatever the causes are, they happen.
This (may) be fixable [I have not been able to prove this outside my own 3DS].
Follow the instructions found in my signature
here. Look for the post called "
How to Properly Setup Anemone3DS when Changing Allocation Size".
You can skip steps 1, 2, and 3 as you're not or haven't reformatted the SD card. I make no promises that it will work in fixing your problem.
Skip steps or adjust according as you only have 3 themes.