Fairly sure R_ChooseOption had been updated before I started to run the script.
With the new version (and updated bank.simba), it logged out in the altar after crafting the runes and walking back to the portal (when I logged back in I could even see the portal).
Edit: I think lately the servers might have been lagging or something for me since I was in the login lobby (where you "Click here to play" or w/e it says) probably from getting "connection lost". I also saw it go to the altar without any essence again, but this could be from lag, IDK.
Sorry I'm not of any more help.
Edit2: Saw it go to the bank, wait a while with the cursor on the scroll bar (even when it was at the top) and then proceed to misclick the essence (just under it) and that was why it did not withdraw any essence. And another proggy;
Progress Report:
**************************************************
Krazy_Meerkat's Varrock Earth RuneCrafting Script
**************************************************
Running for 5 Hours, 49 Minutes and 23 Seconds
Current Task: Walking to Altar
Banked 2604 Earth Runes
Gained 2 levels
**************************************************
Edit3: When it logs out at the altar on the way back to the bank, it is stuck in the repeat until loop on line 427. I believe it is because of the 4 torches.
The script also turns run off when banking.
If you get a strange box the script can loop trying to deposit them into the bank I believe.
Another proggy;
Progress Report:
**************************************************
Krazy_Meerkat's Varrock Earth RuneCrafting Script
**************************************************
Running for 4 Hours, 42 Minutes and 34 Seconds
Current Task: Walking to Center
Banked 3472 Earth Runes
Gained 2 levels
**************************************************
[Reflection Anti-Randoms] 'Evil Chicken' Combat random detected! Running away...
[Reflection Anti-Randoms] 'Evil Chicken' Combat random detected! Running away...
[Reflection Anti-Randoms] Mysterious Old Man random detected! Solving...
[Reflection Anti-Randoms] Solved Mysterious Old Man random!