Does target order in kernel build makefiles matter?

This first line of my arch/arm/mach-omap2/Makefile is

# Common support
obj-y := id.o io.o control.o mux.o devices.o serial.o gpmc.o timer-gp.o
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but it is being ignored by the kernel build system. Only when I move this line to the end of the file do the targets get built. Could another line in the Makefile override the first?

Yes.

Look for another line that assigns a different value to obj-y. If you don't find one, try moving that line to the middle of the makefile, and see if the targets get built; from there you can do a binary search.