Retested with Yellow Runes just now ...

1 Burliness lvl 5 and 1 Flintiness lvl 3, Burliness went into the Flintiness.
1 Preciseness lvl 4 and 1 Burliness lvl 3, Preciseness went into the Burliness.
1 Advantage lvl 6 and 1 Bane lvl 2, Advantage went into the Bane.

Note: Higher lvl rune was on RHS and Lower lvl rune was on LHS