Is there a quick and easy way to reorder de-interleaved data?

Question

I am collecting 5 channels of data through a DMA FIFO by interleaving, then recording to a TDMS file. When I check it, it's in mostly good order, but there are certain points where the channels get switched. For example, the Channel order when I open the file is 1 2 3 4 5, as expected, for several thousand elements. But at some point, it gets shifted to 4 5 1 2 3, and later 2 3 4 5 1. Left-to-right, they are always ordered correctly, so it's easy to reorder them, but very tedious with millions of elements. I have attached some sample data. I'm looking for A) a way to prevent this or B) some kind of sorting tool or script in LabVIEW or DIAdem that may sort it for me. I'll work on a sorting script in the meantime. 
I am using LabVIEW 2011 Real-time and FPGA 2011, and the standard TDMS open and write functions. I also have access to DIAdem. 
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Attachments:
TDMS import-check analog data.xlsx ‏3807 KB

Answer 1

Sorry for the slow response - 
I've looked at everything, and so far I can't identify the problem. I believe my code is consistent with the producer-consumer architecture. 
On the real-time side, I am reading data from the FIFO and writing to the TDMS in the same loop.
On the FPGA side, analog channels are read, converted to the same fixed-point format with a time stamp in a single-cycle timed loop, and then ordered into the FIFO in a for loop. I have posted the relevant parts below.
I am using C-series modules in a CompactRIO.
Attachments:
top-fpga loop-bottom-rt loop.png ‏26 KB