It's normal for this release of TWL Loader. It uses nds-bootstrap to load retail games and it must code all of the NDS functions and commands for all the games to work.
Here is a compatibility list:
https://docs.google.com/spreadsheets/d/1M7MxYQzVhb4604esdvo57a7crSvbGzFIdotLW0bm0Co/edit#gid=0
nds-bootstrap will be updating through time and let more games to be played (eventually be able to save, right now it looks for an official inserted cart to save, I recommend not having any DS cart inserted in your 3ds). If you have the latest release of TWL loader you will get automatic updates for both TWL and nds-bootstrap. I recommend checking every week the software to see if anything changes.
Last week I tested 999 and only got a white screen. I turned it on yesterday and after updating I got it to go past the white screen and to play a menu sound.