If you navigate to a different NetSuite domain than the one you're currently logged into (which is the situation it sounds like you're describing), then you don't have an active login session on that target netsuite site, so you have to log in again. Logging into a different netsuite domain (for example if you are logged into system.na2.netsuite.com and you click on an email that links to system.netsuite.com), will kick you out of the one you're on, so your netsuite user is only logged into one netsuite datacenter at a time.
to fix this, make sure the links in the emails you send out, point back to the netsuite domain that sent them.