The sentence structure I wonder [X] is declarative. The X is usually a noun clause that is the object of the verb wonder.
The X is treated as a thing, not a question. In the sentence
I wonder when my money will be refunded
the clause when my money will be refunded refers to a discrete concept, a particular defined period of time. Overall, the sentence is not asking a question but observing what the speaker is thinking about.
I often think about the possible date of my tax refund and how I am going to spend it (although I don't know exactly when that will be).
Because English is a little-declined language, word order is generally used to reflect which terms are the subject and objects (and other forms) in a sentence. The most common word order is subject-verb-object. To indicate a question, we often reverse the subject-verb order
I will go to the store.
Will I go to the store?
In examples 1 and 3 in the question, the when clause uses the interrogatory structure of verb-subject, will my money and is my money.
As noted above, the object of I wonder is a defined thing, not a question. as such the interrogatory forms are not correct. The declarative forms of 2 and 4 are.