Google has just closed the issue of slow clock problem yesterday, December 13th. As per android authority, google has solved the bug that slowed down the clock on some devices just after they have update to Android 6.0 Marshmallow. The issue ticket was opened within the three days of the first Marshmallow updates roll out.
Some users have complained that Marshmallow is slowing down their clock. Issue no. 189789 was just closed, which was opened for the slow clock issue on October 13th. Still some people think that their clock is falling behind. But as per google, "the case is solved".
Google is rolling out the new update with the bug fixes. I have got the OTA update today on my Nexus 5. Gradually it will be on your device too. Let's keep finger crossed and see if it fixes the bug.
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