I ran into the some problems a while back when setting up connection pooling on Tomcat on Gentoo. It turned out that this was a known issue to Gentoo when using the Gentoo packages.
To remedy this, I had to do:
# cd /usr/share/tomcat-6/lib
# ln -s /usr/share/commons-dbcp/lib/commons-dbcp.jar
And override the data source factory in the Resource definitions in my server.xml:
factory="org.apache.commons.dbcp.BasicDataSourceFactory"
instead of the default:
org.apache.tomcat.dbcp.dbcp.BasicDataSourceFactory
