[Sync] Sync.ConfigureTime_Long.OK shouldn't accumulate multiple configurations

DataTypeManagerImpl::configure_time_delta_ accumulates configure time from
multiple configurations resulting in incorrect counter value.

R=maxbogue@chromium.org
BUG=662598

Review-Url: https://codereview.chromium.org/2484903003
Cr-Commit-Position: refs/heads/master@{#430765}