I wonder if there is an easier way,to get between Avignon and San Sebastian in June. I'm seeing a 10 hour train ride. The plane, goes through Barcelona with a long layover, so is just as bad. We are renting a car in Avignon and planned on turning it in and renting another one in San Sebastian, I've heard that crossing borders with a rental car is very expensive. Any help appreciated.

crossing the border is not expensive. It is the repatriation fee if you do a one way hire that is.
When driving a car you have to include tolls and fuel into your costs too.
If you want to hire a car on a one way rental then drop it off in France and take the train across the border.
This poster can also help you cross the French border.
http://www.fodors.com/community/profile/biarritztaxi/

It doesn't cost anything to cross the border in a rental car. You pay extra if you drop off the car in another country. Is San Sebastian your final stop? Are you flying home from there? If so, you could possibly drop the car in Biarritz and take the train to San Sebastian which is 1.5 to 2 hours.

Vueling flies Marseilles to San Sebastian.
www.vueling.com

Where will you go after Donostia/San Sebastian?

If you go back to France, you will have no rental car problem at all.
If you go to Spain, you may try to give back your car in a French border town like Hendaye, only a few miles from Donostia/San Sebastian.

The typical drop-off fee for a compact car is about €270, depending on the agency. Weigh that against the cost of flying one-way. The best flights are through Barcelona, 7+ hours, for about €193/person, one-way.