Fix that seeking was wrong if frame time was modified

The trjconv -t0 option causes fr->time to be modified and
this then causes the skipping to be incorrect. Alternative
we could document that fr->time shouldn't be modified
and change that trjconv makes a copy of fr before changing
time. This change has the advantage it is less likely
to reintroduce the problem.

Fixes #1405, #1406

Change-Id: Ibd692dfecdf175450fc43f7f35b774bf4446b316