I have looked at this issue and added a connection validation method to the pool which will allow you to execute a query over the connection every time it is taken from the pool. If the query fails the connection is thrown out. This is then repeated until a working connection is found. If no working connections are found, a new connection is made and returned.
This feature wil be in 2.0 RC5 and should solve your problems if you do not wish to turn off the connection timeout.
.
Check the servoy administration servlet (usually at http://localhost:8080/servoy-admin when you are running the developer), under DB Servers.
Hope this helps.