In Windows Server 2008 R2, if the Provision a Shared Folder Wizard is used to share a folder which has a folder quota defined, the quota’s source template is reapplied. If the quota did not match its source template, the quota settings will be changed unexpectedly. If the quota was not created from a source template, the first available template will be applied.
You can select a particular template to apply instead of the source template/first available template, but you cannot prevent a template from being applied.
To work around this problem, create a template that matches the quota on the folder being shared before running the Provision a Shared Folder Wizard, and select this template at the appropriate point.