As already stated I would look for errors on both sides of the like Cisco and Juniper. If the uplink is a dot1q trunk make sure you turn off dtp and switch port negotiation on the cisco side. I've seen interface erros from not doing this.
After that look for obvious erros via Wireshark on whatever host is having the problems.
You can manually trace the path of things if you need to to by looking at routing and mac address tables.
Also, listen to rccpgm He knows what he is talking about.