CMS2CMS counts only existing unique content pages of your website. Google Webmaster Tools shows the number of all indexed pages, which iclude pagination, login/sign up pages, 404 pages etc. Moreover, the same page with and without www. in the domain address is considered to be two different pages by GWT. This is the reason why the quantity of migrated pages and existing ones according to GWT is different.
You don’t need to worry as all of the content from your previous website has been migrated to the new one.