RXtools glitch?

I run rxtools with the MSET exploit on sysnand 4.4 with a 10.3 emunand. Whenever i go onto settings while on emunand it shows Ver.10.3 and not RX10.3 like it used to. I'm sure when i did everything the first time it was working and now when i use rxtools on sysnand it shows RX4.4. Could rxtools think my sysnand is my emunand and viceversa? Is there a way to fix it?

EDIT: Forgot to mention all .cia installed on emunand still work