The memory configuration parameters are set inside a extremely tiny SPI flash memory on each RAM module. A 1333MHz module have different configuration parameters for different processors (there are Nehalem/Westmere Xeons with memory controllers that run at 800/1066/1333MHz) and will work at 800/1066/1333MHz depending on the Xeon model installed.
Apple sold 1066MHz Xeons with all single CPU Mac Pros and most of the dual ones. Almost all Mac Pros manufactured after sometime back in 2010 have from factory 1333MHz DIMMs, the memory industry changed from 1066 to 1333MHz RAM very fast - even some early-2009 have from factory 1333MHz DIMMs but a 1066MHz Xeon.
When the memory controller is initialized for the first time, the DIMM SPD SPI flash memory is loaded via I2C protocol and the appropriated configuration parameters are saved inside the NVRAM, one MemoryConfig variable per memory slot. Also is saved a cache of the SPD, since loading it via I2C at every boot is extremely slow.
So, there are situations when you have 1333MHz DIMMs with a 1066MHz Xeon running the memory at 1066MHz and since the memory parameters are still set/cached inside the NVRAM, if you later change to a 1333MHz Xeon, the memory controller still runs at 1066MHz since it's what are stored inside the MemoryConfig variables. Please note that this is only valid for dual rank DIMMs, 2Rx4. DIMMs that use quad rank configuration, 4Rx4, will run at slower frequency - it's a design limitation of the Nehalem/Westmere memory controller.
To solve this issue you need to do a deep reset of the NVRAM, doing a 4-times continuously NVRAM reset with a wired keyboard. Power-on, then press CMD-Option-P-R and only let go of the key combination after you hear the 5th chime.
The deep reset forces the re-initializion of the memory controller data saved inside the NVRAM variables, the cache of the SPD and if the Xeon and the DIMMs support 1333MHz, it will be the frequency used from now on.
