Fix problems with rtc_linux.

Fix problems with rtc_linux.

2) Changes to rtc_linux.c which a) do a double read of /dev/rtc when the
PPM interupt is turned on after the wait time expires. The current read
does not block to the second, as it should, thus two reads are needed.

Also, changes so that at startup the system properly ignores the last
system time from the initial burst mode for setting the system time since
it can be way off. At present this last system time is included in the
regression, which throws it off until finally that sample is dropped.