So I have just had a bit of a play. First off it appears there is no cache even on PXI RT. I have just tried this and disabling buffering throws an error.
I still can't understand the periodic jitter you see but I suspect you may be pushing the boundries of the HD write speeds. I have just tried a similar set up on an PXI-8106RT and the fastest I see is 12ms for the 512kB files as you are writing, based on what you said we need to hit 10ms. Of course newer targets may be able to achieve more.