  We report the pulse timing analysis of \emph{Rossi X-ray Timing Explorer}
(\emph{RXTE}) observations of the anomalous X-ray pulsar 1E 2259+586 from its
2002 outburst to October, 2010. Our objectives are to extend the work on the
recovery stage after the 2002 glitch, investigate the variations caused by the
second glitch which occurred in 2007 and look for other unusual events, if any,
that arise in the regular spin-down trend of the source. The recovery of the
2002 glitch gives good fit when the two-exponential glitch model of the Crab
pulsar is used, rather than the standard glitch model, in the 1360-day interval
after the first glitch. The sampling of the following 260-day is not frequent
enough to be phase-connected. After that interval, our timing analysis yields
that there is a fractional frequency change of
$\frac{\Delta\nu}{\nu}\sim8.20(2)\times10^{-7}$. Moreover, we report two
frequency shifts of fractional changes,
$\frac{\Delta\nu}{\nu}\sim3\times10^{-8},-1\times10^{-8}$: The first one at MJD
$\sim53750$ had a positive fractional frequency change in contrast to the
second one at MJD $\sim54880$ for which the pulse frequency decreased. These
frequency shifts both resemble the microglitches observed in radio pulsars.
