Are you launching it directly from there or getting it into the Homebrew Launcher through Browserhax? I'll assume it's the first. In which case, you should really get menuhax setup.
I actually answered something similar to your situation, so I'll just copy and paste that here:
Setup autoboot menuhax, through browserhax.
Steps:
1. Put the contents of starter folder from the starter.zip (
http://smealum.github.io/ninjhax2/starter.zip) onto the root of your SD Card.
2. Change your theme 2-3 times, from default stock one to any other, and finally back to default stock one.
3. Open the browser, then open the browser settings as fast as possible, scroll to the bottom and Initialize Savedata or Clear All Save Data, as fast as possible.
4. Navigate to
http://yls8.mtheall.com/3dsbrowserhax_auto.php (Keep trying until it works)
5. Open the menuhax_manager app.
6. Press A to install. Just look for a success message towards the end to know it was successful, disregard any errors messages that may appear prior to the success message.
7. Go back to the main menu of menuhax_manager, and go to then select "Configure/check haxx trigger, Press A to continue, then select "Type1"
Either:
A) Don't hold any buttons and touch the bottom-screen for autoboot menuhax, or
B) Hold the desired button you want to trigger menuhax at boot, and while holding it touch the bottom-screen.
8. Depending on you configured your haxx trigger, will depend on how menuhax launches from now on. Make sure you have rxtools.3dsx in an rxTools folder under rxTools to launch it from menuhax, after it load the Homebrew Launcher.
Consider using CTRBootManager and setting it to autoboot rxTools (or Luma3DS if you switch.)
Link:
https://gbatemp.net/threads/ctrbootmanager-3ds-boot-manager-loader-homemenuhax.398383/
Consider switching from rxTools to Luma3DS.
Guide:
http://gbatemp.net/threads/tutorial-updating-from-rxtools-to-luma3ds.427735/
Or at least consider switching to dukes_rg fork of rxTools.
Link:
http://gbatemp.net/threads/pre-release-wip-yet-another-rxtools.426092/
Menuhax does have a failure rate of launching properly, consider A9LH if you must have 100% bootrate, but it's a pretty long guide and can take a while to setup properly, ask questions if you need help.
A9LH Guide:
https://github.com/Plailect/Guide/wiki
Enjoy your new setup without having to rely on browserhax, whether you decide to go the menuhax route or A9LH route~!