There are few things one should consider:
If there current Sitecore installation is upgraded from 6.4 or prior version to your current version; the item's layout deltas might be an issue. You will have to check the raw values of the Layout details field and figure it out.
Any changes made on the Layout Details on Standard Values do get cascaded down to the items created from that specific Template.
If you don't want these changes to get inherited try multiple inheritance. And change the template of those items created.
Lastly, if the above doesn't work, try creating a new template with the changes you want and change the Template of those items created.
Hope the above helps. Share any further questions you might have or even if the above haven't answered your questions.
Happy Sitecoring!