I've tried adding it to the whitelist:

gsettings set com.canonical.Unity.Panel systray-whitelist
"['JavaEmbeddedFrame', 'Mumble', 'Wine', 'Skype', 'hp-systray',
'junglediskdesktop']"

This sort of works - you end up with three icons (one for each Jungle
Disk state - connecting, inactive, active), but it is usable.

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https://bugs.launchpad.net/bugs/751171

Title:
  Jungle Disk unusable - no indicator icon

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