My TronicalTune wont store my custom tuning E2, B2, E3, E3, B3, E4. Is there a solution for that??

Due to the limitation of two same notes with adjacent strings, TronicalTune does not allow to store that.
But it works with a small trick, here is the how to do that:

First part A): How to teach in the frequencies.
1 – Tune to standard tuning red bank “E”.
2 –  Enter single string mode and move with cursor to the “G” string, now fret the G string at the 3rd fret as accuarate as you can and plug the string, let ring 3 to 6 sec.
TronicalTune will tune down that string to E3 at 164,81 Hz.
When the “G” LED is green switch off the system, fret the G-string at the 3rd fret again and retune to standard tuning in multi string mode in the same manner you normally do.
3 –  Now enter custom tuning mode and teach in the frequencies as follows:
Plug low E-string until “E”-LED is green, then MUTE all strings; Fret A-string at 2nd fret and plug until “A”-LED lits green, MUTE all strings; Fret D-string at 2nd fret and plug until “D”-LED is green, then MUTE all strings;
Note: you have stored the frequencies as follows; E-string = E2; A-string = B2; D-string = E3. The system will not allow to store E3 with the G-string now, but no worries:
4 –  Fret the G-string at the 2nd fret now (F#3) and plug it, let ring 3-6 sec. until “G”-LED is green; plug B-string free until “B” LED is green, plug high e string until “e” LED is green.
5 – The blue “E” LED will be flashing now, if you want to store at that position in the blue bank push “Enter”, if not move with cursor to any other preset position (E, A, D, B, G or e) prior to pushing “Enter” to store.
We will store at blue “E” for this example!
Afterwards the above notes are stored at that position. Remember that you MUST fret the G string in the 2nd fret in order to get the right note with the G-string (F#3 to get E3 with unfretted G-string).
Now the notes are stored, but the system has to learn how to get there first, we will do this in “Single-String-Mode” a follows:

Second Part B): How the system learns.
Do the following please:
1 – Enter blue bank “E” (or your respective preset position) and press and hold  “Enter” for more than 2 sec. to get into “Single-String-Mode”.
2 – Plug the low E string and let ring 3 to 6 sec. until “E” LED is green = in tune, then MUTE ALL STRINGS; Now plug the A string and let ring 3 to 6 sec. until “A” LED is green = in tune, then MUTE ALL STRINGS;; Plug the D string and let ring 3 to 6 sec. until “D” LED is green = in tune, then MUTE ALL STRINGS; Fret the G string at 2nd fret, plug it and let ring 3 to 6 sec. until “G” LED is green = in tune, then MUTE ALL STRINGS; Plug the B string and let ring 3 to 6 sec. until “B” LED is green = in tune, then MUTE ALL STRINGS; Plug the high e string and let ring 3 to 6 sec. until “e” LED is green = in tune, then MUTE ALL STRINGS.
That is close to your desired tuning now, but due to neck relief in single string mode it might not be very accurate, therefore

Third Part C): How to refresh in Multi String Mode.
3 – Enter your tuning in “Multi String Mode” by pushing the “ON” button once, the last completed tuning should come up to be “refreshed” in Multi String Mode (indicated by flashing blue “E” LED right after pushing “ON” button)
4 – Now fret the G string at the 2nd fret and strum all strings simultaneously, let them ring 3 to 6 sec., mute and keep dampened strings that are in tune already (green LEDs) and plug the ones that are still red only.
Keep the G-string fretted at the 2nd fret all the time. Once the system switches off, the free ringing strings will be tuned to your tuning: E2, B2, E3, E3, B3, E4.

Some additional notes:
I want to mention that every time you want to tune to this tuning you MUST fret the G-string in the 2nd fret.
When you are tuning to this tuning and you come from another preset that does NOT require you to fret any string, then you should tune in single string mode first, and afterwards refresh in multi string mode.
If you are tuning from this tuning to another preset, TronicalTune will most likely switch to single string mode for the G string, because the memory expetcs the G string to be at F# and not at E3….

There are way more possibilities if you know what you are doing and how to approach different open tunigs in the best way