I am not from Intel, but I believe you are describing the Linux behavior which by default changes the CMOS RTC to store UTC time instead of local time.
Either you can change your wakeup time (and initial setting of clock in CMOS) to be in UTC (rather than local),
or you can do something like the following steps (in Ubuntu):
gksudo gedit /etc/default/rcS
modify the line that says UTC=yes
change it to say UTC=no