Latest 3.17 kernel was installed on Utopic to test this problem.

Behaviour is the same.

External HD is recognised only first one or two times after booting the
system.

Similar errors as with previous kernels are reported in dmesg then. I
noticed that they slightly differ if the disk is connected directly to
USB 3 port or through USB 2 powered hub.

The disk in this enclosure works properly  when connected to MacBook Pro
laptop.

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https://bugs.launchpad.net/bugs/1378401

Title:
  External USB3 hard drive fails to connect (JMicron bridge 152d:0569)

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