Do you go straight to system settings after starting up emunand?
The RX-E thing is actually just a string of digits that don't mean anything, and there are a couple actions that you can do while in emunand that will unload that RX-E from memory and you will be back to displaying Ver. in the system settings.
As long as you are sysnand 4.4 and your MSET exploit is working and loading rxTools then you are in rxTools, regardless of if it shows Ver. or RX-E in system settings.
In fact, CakesFW doesn't even modify that Ver. string because it isn't needed. Only thing it's used for is to make it easier for the end user to confirm they are on emunand. But you know that your sysnand is 4.4 and you know your rxTools is working and loading a 10.3 emunand.
A few actions I have found affect the RX-E string are, entering Badge Arcade and running DevMenu (or BBM) once. If you do that, even just once, then entering system settings will just show Ver. instead of RX-E.
There have been times though where I could have sworn I entered system settings first thing after booting emunand and it showed Ver. I could just have been distracted and forgot I did things though. Also there are a few actions within system settings that don't throw you back to sysnand, but remove the RX-E and you are back to Ver. You are still in emunand though. One of these being accessing NNID settings, you'll be back to Ver. once it puts you back in system settings. But that's just a visual thing and doesn't affect the plethora of patches you have running and you are still on an emunand running off the SD card.
The RX-E string is actually loaded only once, and once you've seen it once then the Ver. string is restored. I don't know if the same thing happens with GW.
