I am using Mage::getSingleton(“customer/session”) to be able to login to Magento externally. Problem is, this seems to clear up other $_SESSION variables I have set.
How can I have the entire cake and be able to login to Magento plus setting normal SESSION-variables?
I assume this answer might apply to you also: Magento external login will not create session cookie
In essence try first creating the Magento session before you create the other session.
If that doesn’t help you might need to provide additional code so a good answer can be supplied.