Which version of Fuse ESB/ServiceMix are you using? There have been some improvements to the JNDI code in 4.2.0-fuse-02-00 and 4.3.0-fuse-00-00 so if you are not already using those versions you might want to try them.
I would not expect such issues in 3.x because we have many users with the same use case and we have had no major issues with JNDI in a long time.
I am using FUSE 4.2-02-00, It seems there is some issue with the JNDI look in this version.
Can you please tell me what is wrong with this, the JNDI look up for the connection factory getting timed out...