Sounds like the two files are fragmenting each other while you're writing them.
Some ways to check are
1. Write both files to an empty partition (if they're fragmented it must be with each other since there aren't any other files)
2. Write only one of the files (if it's not fragmented then the other file must be what's fragmenting it normally)
Assuming the above is the case (seem likely to me). Then it's caused be the os not knowing how much space the files need, so it'll put them right next to each (as well as the chunks needed as their requested).
I don't see this being a real problem though. But if you want to try to fix it anyway.
1. If you know the size before hand (I've not tried this so I may be missing something) you could open one file allocate the size with the set file size vi, then do the same for the other file (this is before you start writing the files) . Note this could slow down the effective hard drive speed since it has to seek back and forth to each file (I doubt you'll notice though).
2. Write each file to a separate partition. This has the same seeking issue as 1. but you don't need to know the size before hand.
3. Write each file to a separate hard drive. This needs a second hard drive but is the fastest and simplest solution.
4. Write both data stream into the same tdms file. Tdms is nearly as fast as binary, has data structure, can handle having two things writing to it at once, and you can defrag the single file (via tdms defragment) if you really care about it's reading speed (this is likely much faster than a windows defrag), and as far as windows is concerned it's not a fragmented file
