Hi,
Based on your description, my suggestion is as the followings:
1. Confirm the time zone setting in the "Web Application General Settings"
2. Confirm the regional setting in the root site of the site collection, be sure that the "All sub-sites inherit these Regional Settings" need to be set checked.
3. Then go to the corresponding subsite's regional setting, and confirm the settings there.
Here is a similar thread for you to take a look:
http://social.technet.microsoft.com/Forums/sharepoint/en-US/63344765-98ac-4fc8-afab-408a7b25db4a/connecting-outlook-to-a-sharepoint-off-sets-time-by-3-hours
Please inform me freely if you have any questions.
Thanks