I am not sure whats the problem then. I use lammps custom dump.
I had the same issue when I used multiple processors but worked fine when I used single processor when using the rerun command. I did not report it though and I am not sure if the problem still persists With the current version of lammps.
I am guessing you are using a rigid water model. Have you invoked fix shake while using the rerun command.
Good luck
Arun.