make sure all pixel rejection settings are turned off, i think "clip low range" is on by default and may be active even if pixel rejection is turned off.
beyond that i don't think i've ever seen this problem with integrating 3 masters (but i have seen similar artifacts when integrating subs). one thing i'd try, but might be sort of a hack, is to linear fit 2 of the masters to the highest SNR master and save those masters, then see what happens when integrating them.
rob