For example:

% cat t.hs
f x = x * 20
main = print (f 20)
% cat pp
#!/bin/sh
cp $2 $3
% ghc -fhpc -F -pgmF./pp t.hs
[1 of 1] Compiling Main             ( t.hs, t.o )
Linking t ...
% cat .hpc/Main.mix
Mix "t.hs" 1308170257 1934109072 1 []

If I omit pgmF, then I get proper Boxes in the .mix file. When I run over a large code base, some scattered expressions get Boxes, but the majority don't.

I think this started showing up with ghc 7.