Question
The liner comes up after heavy rains. Water goes between the bottom soil and the liner. If I raise the lip around the pond, I think I'll have more of a 'boat' effect. If I lower the it, then I'll have rain water, mud, and contaminants going into the pond.
The soil is basically hard clay, thus drains slowly. It takes several days after a heavy rain for the liner to go back to normal.

Answer
See http://www.fishpondinfo.com/ponds/pcare2.htm#liner where I wrote a little bit on liners coming up.  If this happens all the time, you'll probably have to put in a drainage system around the pond if it's due to runoff or under it if it's due to a high water table and slow drainage.  I wish there were a simple answer!  Good luck!

Robyn