Heidi,
What version of ClickDimensions do you have installed? Our current version is 6.0.0. When you reactivated all ClickDimensions plugin steps, if you have a version prior to 4.2.0, you would have also enabled some steps that are no longer in use and that can cause visits to not be recorded properly.
You can check your version by going to Settings > Solutions. If the ClickDimensions version is older than 4.2.0, you can either:
1) Update to our newest version. See the 2011 tab on this article about using Auto-Update: http://help.clickdimensions.com/automatic-updates-to-clickdimensions/
Choose the first or second option from the Auto-Update dialog; or
2) Disable the following deprecated plugin steps per this article: http://help.clickdimensions.com/february-2013-release-manual-steps/