I've located my rear junction box just in front of my bottom bracket. I dont feel right allowing it to flop around freely within the frame. What are the bike shop mechanics or anyone doing to prevent this? The inside of the frame is pretty rough, so I dont see how double stick tape will be effective plus its pretty difficult to get my fingers in there to make that happen.
Any ideas would be greatly appreciated.

Bluetak? It's a gummy type stuff used for sticking posters to walls etc. Infact I don't see why Chewing him itself wouldn't work?

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http://weightweenies.starbike.com/forum/viewtopic.php?f=10&t=100739

Hot glue from a glue gun?

Although you are overthinking the problem, put some zip ties around the wires and near to the connectors. A thin layer of form around the JB itself keeps it from un-rattling.

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Scott Foil Ultegra Di2
Scott Scale 35 26"
Scott Spark LTD 29" M8000

As above, wrap it in a little foam, corrugated cardboard, whatever. Zipties around it or the wires, with the extra ziptie length sticking out like antennae, will keep it pinned to a wall without rattling.