Same situation here. When running 3 sticks, I got 1333, but only 1066 when use all slots. (All 4 sticks are the same)
Anyway, after some tests. It's no way to tell the difference in speed for normal real world usage.
For benchmarking, yes, triple channel will shows better result. However, for real world usage, more RAM usually will win (because more cache avail for the system).
So, if 48G is good enough for you, of course you can run them in triple channel configuration. However, if you able to use all of them, that means go for 64G is the better choice. Otherwise, if the system start to use HDD because running out of RAM, that will be 1000 times worst than running the RAM in 1066.