Variation between single-threaded runs

I'd expect results of successive runs, at least on a single thread, to be identical. However, I see some differences. These vary from run to run, so perhaps something's being used uninitialised. I'm using the comparison script from the position_cache branch, which just does a brute force comparison of - by default - coordinates and velocities. After a build, from the examples/ directory:

git checkout origin/position_cache validate
./test_fixdt -r 2 -t 1 -f SodShock/sodShock.hdf5 -m 0.01 -w 5000 -d 1e-4
mv output_002.hdf5 A.hdf5
./test_fixdt -r 2 -t 1 -f SodShock/sodShock.hdf5 -m 0.01 -w 5000 -d 1e-4
mv output_002.hdf5 B.hdf5
./validate A.hdf5 B.hdf5 
# says e.g. 993745 changes, up to 1% (I've seen up to 4%.)

I can't reproduce this at all with -r 1.