This is not retroactive so all comments you made previously will still be linked to the first blog. Is the second blog registered to the same username that the first blog was or not?
If it is registered to the same username try this first > clearing your browser cache and cookies. Then try this again Dashboard -> Users -> Personal Settings -> then scroll down to Account Details. Then scroll down to where it says ‘Website‘ select the URL for your primary WordPress.com blog and then save changes.
If that does not work for you then you will need Staff help. Here’s the link http://en.support.wordpress.com/contact/ After you use the searchbox, under the search results, at the bottom of the page there will be a section that says “Have you found the answer to your question?” You can choose either “Yes I found the answer to my question.” or “No I didn’t find the answer to my question and I would like to contact support for help.” The no option will reveal the contact form.