Are you turning the flares enough after you push them in? I find that after I push in the flares on mine and turn them clockwise to keep them from popping back out, the red rods can be pushed in so that they're flush with the rest of the armor and then the flares can be further turned a few more degrees to keep the red rods from popping out again.
I thought that was the standard procedure. Works for me.
Yeah quite surprised that this is seemingly an issue... I have not check MIV instructions but it was mentioned in MIII BD instructions as well so might want to take a look at it folks