I have exactly the same problem, and have had to stick with the JDBC-ODBC bridge.
I'd be grateful for a solution too.
I’m running against a DB2 database on an AS/400 (iSeries) machine. I’m using the latest JTOPEN driver (6.5.1) and have tried both 3.0.1 and 3.0.2 of SQuirreL.
I can connect, download the tables, and run statements. But if I leave the session idle for few seconds, say 30, the connection is lost. I have tried against two different hosts with the same results.
Using the JDBC-ODBC bridge work fine, except that it seems to reports phantom errors after some statement complete correctly, and I think the JDBC driver would solve some of this.
If anyone has any suggestions on how to fix this problem I sure would like to hear from you. SQuirreL is a great product at a marvelous price.