Comment 4 for bug 504440

Jouni, the problem is with internal readers, which cannot be reconnected without disassembling the computer.

Also, the description says "Drive worked fine until last couple of weeks": do you mean that this has been a regression in a Karmic update? This is not my case: since the release of the "safely remove" option I am experiencing that it disconnects the internal reader. "Eject" option works well.
It is really disturbing, but only the first time, until the user learns that safely removing that drive will disable it until next reboot.

Actually, as mentioned in bug #404185 (eject working as safely remove) the key point is to identify internal devices and do not offer the option to "safely remove" them, but this is quite difficult as they are usually connected through USB (an internal USB port) just like external devices. Another possibility could be to enable a reconnect signal for repowering up the device without actually disconnecting the cable (though I am not sure if the USB controller allows this).
In that case, I think that possibly linux and devicekit packages are also affected by this bug.