Plink 1.9 --merge-list changing order of fam file
Thanks Christopher Chang for the great answer via the plink2 google group! (See here)

His answer was as follows:

"Yes, plink 1.9 did change the default merged sample order.  However, you can request plink 1.07’s behavior by adding “--indiv-sort 0” during the merge.  (You can also use --indiv-sort + --make-bed at any time to change the sample order to whatever you want.)

As for why the default was changed, take a look at the new default order: it will probably make a lot of sense.  It’s “natural-sorted” which tends to make it easy for humans to manually search through regardless of what mix of letters and numbers are used in the IDs."

See also the Plink 1.9 documentation for --indiv-sort which makes the point that this behavior is default only for merges--in other commands Plink 1.9 uses the same ordering as in Plink 1.07, which is the order the samples were in.