I have a Bangkok Bank account I do all my monthly spending out of and also a KBank account for my money I need for my visa. I could have used just one account for both, but decided not to, and it’s worked out for me.
That does sound like an issue. Maybe you can ask the embassy if you can show them in your Thai bank account. I’m not sure. Worst case scenario is to wire transfer them back to your bank in your home country and then wire them back to Thailand when you move.
When you’re applying from your own country, you show the funds in your bank account from your country, not from a Thai bank account. That’s only for when you’re in Thailand.