This is my guide from reddit, it looks like it helped lots of people so I decided to post it here. I also have made some modifications.

This works for both the Old 3DS and the New 3DS, however it may not work with all CFW's. I am using ctrbootmanager and CakesFW and have a 100% boot rate.

This is for 9.2 CFW users who are having issues. If you aren't having issues, don't bother fixing whats not broken . I don't know if the older payload will work on 10.3 I haven't tested it as I use menuhax on 9.2 to autoboot my CFW.

This might only work on the N3DS thats what I have and it has improved my boot rate a ton.

Step 0: install menuhax normally

How to install:
1) Download this file

2) Copy the files from the 3ds folder it to the 3ds folder on your SD card

3) Boot it in HomebrewLauncher

4) Install (make sure you are using themehax manager)

The rest is optional however if you want autoboot you must continue(otherwise you must press "L" to boot menuhax)

5) Connect to your PC and copy "menuhax_ropbinpayload.bin" from your sd card(this is the old payload)

6) Install homemenuhax like normal again.(this will replace the old payload with the new one that doesnt work well on 9.2)

7) Reconnect SD to PC and look for the new menuhax payload(mine was named: ropbinpayload_menuhax_USA23552_new3ds.bin)

8) Copy the name of the file(in my case "ropbinpayload_menuhax_USA23552_new3ds.bin") and rename "menuhax_ropbinpayload.bin" from earlier to the new file name

9) Replace the file on your SD card with the renamed payload on your PC.

10) If done correctly the screen will flash white, blue, and red the easiest way to tell is that there is no yellow screen.

11) Observe boot rates nearing 100% \

Remember selecting install in MenuHax installer will replace the old payload with the newer unstable one!


I do not know why this works. My guess is that the new menuhax was made to work on the latest 10.3 not for 9.2. On reddit some said that menuhax worked fine for them on 10.3.
Credits to mid-kid he told me how to do this on IRC.

 

Unfortunately no way to change the bottom screen .

 

Yeah that is useful as it does show the different stages of the hack. Using the older payload though I haven't had a failed boot yet(at least caused by menuhax, my CFW still fails to load though probably because I use 10.3 emunand on a N3DS)

 

Messed up my menuhax etc. hard. Can't even get rxTools working again. Thank god I made a copy of my sdcard earlier today so I can restore this mess.

 

Glad it works!

 

For me I had 50% white screen crashes 10% yellow screen crashes and 40% successful boot with a 50/50 boot chance of CFW so this was very irritating to deal with at first. In the past week CFW updates have fixed many things and I have a fully successful boot 50% of the time. It even works when my 3DS is closed which is awesome!

 

THIS DOESNT WORK
I found an easier way to do this: download the zip, go into the other app payload folder, find the one for your 3ds(if you dont know how use the other method) rename that file to whatever your current menuhax payload is called and replace your current menuhax payload with the new one from the download.

 

Yeah that never really worked for me. Mine is set to X

 

I did it and now on my 9.2 N3DS menuhax triggers everytime.
However, I can't seem to be able to change the sysNAND theme nor set a boot image.

 

Could you elaborate on how to determine which file to use? I've tried two that I thought were correct but alas they were not.