There is a big difference in emphasis. In the first, the adverb "really" modifies the verb "is". In the second, "really" modifies the adjective "true". The word "really" provides emphasis to the word it modifies. We could achieve the same effect by putting the emphasized word in caps: (1) if it ***IS*** true or not (2) if it is ***TRUE*** or not

They are both the same, however some speakers or teachers argue that. "if it really is true or not" is emphasising is it really true. "if it is really true or not" is emphasising "if it is true (really) or not. But this can be considered as just "nit picking"

Putting the adverb before the verb often emphasizes the adverb. However, in this case (to be + really) the meaning isn't really different, so really they're interchangeable.