Update DueTimer.cpp

1. In setFrequency(), _frequency[timer] is stored as the actual frequency rather than the desired frequency. This change is propagated to setPeriod(), which calls setFrequency(). This affects the values returned by getFrequency() and getPeriod().

2. In bestClock(), the formula to compute the error was scaled to the divisor ratio for a more meaningful comparison.
Merge pull request #34 from chrishakim/master

Update DueTimer.cpp