Waking Raspberry Pi on time schedule using Sleepy Pi
I have the same problem and  I just saw that they fixed a bug in a library used by SleepyPi

More specific, the RTC library file DS1374RTC.cpp reads since March: '2015
(which is after the question was asked)


  Releases
    ========
    V1_0 - 10 Aug 2013 - Initial release
    V1_1 - 11 Mar 2015 - Mod:    Added "ackAlarm" and "ackRTCOSF" functions to aid Alarm use
  - Bugfix: Changed the way the "SetAlarm(tmElements_t   &amp;tm)" was updating the Alarm time. It wasn't mapping correctly


They also added a new example to wake up the Pi: WakePeriodicallySimple.ino