No, there are no known conflicts between eCart and Cookies toolkit or with Security Assist which is probably how you have configured the login rather than cookies toolkit.
when you configured the login did you follow the "Applying Register/Login to your checkout" tutorial on the eCart support page:
With security assist, the login is based on a session variable. if the session is not set, then the user is considered logged out.
IT is impossible to tell what may be going wrong with out being able to reproduce the problem.