@Arrowstar I've had a similar problem. Using bodies file and importing initial data from the active craft and then uploading the "perfect" maneuver and it completely misses planetary intercepts. Tried with both stock bodies and RSS and had the same problem. I did a quick check with a completely stock game (no mods) and found that it seemed to work fine - can you try that @jakkarth and let me know if that works for you?
At this point though, I'm not sure if it's a particular mod that messes it up, or if the further it gets from the starting UT the further out of sync it gets. Now that I know I'm not alone, I might do some more testing.