Quoted from rai:On the higher level missions, what's the multicolored shot? You said it gives you medals, does it complete the mode quicker? I seems to have a trouble with the upper level missions it doesn't seem like my shots always count, like I'll make a few lit color shots but my count down number of shots left doesn't always go down. Maybe there's roving shots and I miss the actual shot but I can't verify this since I've not played a lot of upper level missions.
In Tier 2 and 3, the blinking/color cycling shots are required to earn medals, but they count the same as a regular shot toward completing the mode. So you don't want to "waste" your hits on regular shots, blech. But look out, in KB3, the Warp ramp likes to be the blinking shot so it can be tough to earn medals there. One of the best modes is Nero 2, where you try to hit all 3 blinking shots in combo. Alpha ramp, beta ramp, left scoop for 2x bonus jackpot. Some of the modes could use some tweaking to make them more unique, but it's all fun anyway.