Tynon says you need to refresh before you go into the rune temple. Your client sometimes adds coins twice. It seems to do it worst when you are in arena and your stakes are added or when you get rewards for sailing. The amount of money you see is higher than you really have. When the server, which has the correct amounts, sees the difference it makes you refresh to fix the error. You never lost coins or runes because you really didn't have them.
I say fix your code Tynon so this doesn't happen. It costs me gems to use the shrine after I try to save enough coins for my upcoming blacksmith and still buy runes while I wait for the cool down to end. Then find I don't have the 1.5 mil I thought I did. I am broke because your code is broken. Don't say my client,you own the you code you fix it.