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Ah, OK, looking at the source I see that you've still kept the wave structure, I thought you had completely gotten rid of it and then each tick look back to see what wave would hit now over the last N ticks of bullet flight time and retro-actively construct the wave from the conditions as they were then. What you've done isn't quite that drastic =)

As for what is different, have you tried projecting the point back into the cartesian plane and printing it to see if it is the same as the actual enemy location? How about using both types of tracking at once and seeing if they are giving the same results at wave-hit time?