e1000e: fix systim issues

Two issues involving systim were reported.
1. Clock is not running in the correct frequency
2. In some situations, systim values were not incremented linearly
This patch fixes the hardware clock configuration and the spurious
non-linear increment.

Signed-off-by: Yanir Lubetkin <yanirx.lubetkin@intel.com>
Tested-by: Aaron Brown <aaron.f.brown@intel.com>
Signed-off-by: Jeff Kirsher <jeffrey.t.kirsher@intel.com>