They bought (or in some cases leased) their 747-400s new and selected the CF6 over RR
engines. The 747-200s with RR
engines were second-hand and came from Cathay and Air New Zealand. Previously, they had operated still older 747s from SIA (and others?) with PW
So the answer really is that their second-hand 747-100s and -200s came with whatever engines the original operator had selected but their new 747-400s have the GE
engine that Virgin chose.