Having similar problem in 16.04 as well, though the reason might be
different.
With everything enabled this is the output of rfkill:
2: phy0: Wireless LAN
Soft blocked: no
Hard blocked: no
5: Toshiba Bluetooth: Bluetooth
Soft blocked: no
Hard blocked: no
7: hci0: Bluetooth
Soft blocked: no
Hard blocked: no
When either the switch in System Settings or the Indicator menu is
turned Off Toshiba Bluetooth is soft blocked, hci0 disappears, and the
Indicator icon disappears. When the System Settings switch is On,
Toshiba Bluetooth unblocked, hci0 appears soft blocked, and the
Indicator icon appears with it's menu switch Off. When the Indicator
menu switch is On hci0 is unblocked.
It appears that each switch is grabbing the earliest bluetooth radio to
effect rather than just one.
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https://bugs.launchpad.net/bugs/1126108
Title:
Indicator disappears entirely when disabling / turning off bluetooth
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