Are you sure Raikou wasn't already on route 39 when you saved the game? If it was, it will move to a new route. That's what the boxes are for on RNGReporter, you enter their current routes so it will work out if they jump twice.Just wanted to bring up something I noticed using RNG Reporter tonight.
For the seed 1070324 the expected output was Entei 37, Raikou 39, and Latios 28. When I went to check the seed, Latios and Entei were in the right routes but Raikou was in 38. I went ahead anyway seeing as 2 out of the 3 were right and ended up getting my shiny, meaning Route 38 was "right" for Raikou. Might be a programming bug or something but just wanted to bring up that if 2/3 (or maybe even if 1/3) roamers match the expected output it might still yield the desired Pokemon.