fix for random seed XOR and initialization of trajectory_counter

* when nmeas < nsave, nstore is not incremented from run to run and exactly the same random numbers will be used from run to run
* also, trajectory_counter is normally initialized to 1 but it was set to 0 if initialstorecounter was "readin" but no .nstore_counter file was present (or it was impossible to read), this commit makes the two self-consistent by numbering the first trajectory "0" in the default case as well