Try this:
1) Make sure the bridge section actually touches the ground (wether it is under water level or not).
2) Set the height of the bridge section by un-ticking the "Fit to Ground" box and then type in your height.
3) Don't touch it again unless neccesary. If you do have to touch it, repeat these steps.
To be safe I make sure the bridge section(s) is/are where I want it exactly, then save it. Close WRPedit and re-open it to continue work.
Hope this helps,
Waterman.