Answer from Kim:

This is because the migration does not copy the <web-resource-collection> part of the web.xml's

so to fix this problem you can simply copy the part from you old web.xml's into your CLM applications files and your applications will start doing the correct redirect upon login one by one.
It could look something like:
<web-resource-collection>
   <web-resource-name>secure</web-resource-name>
   <url-pattern>/authenticated/identity</url-pattern>
   <url-pattern>/secure/authenticated/identity</url-pattern>
   <url-pattern>/web/loggedInUser</url-pattern>
   <!-- This URL pattern is a work-around so that older RQM clients can log into RQM 2.0 servers without modification. This line should be removed when there are fixpacks available for the older clients -->
   <url-pattern>/secure/service/com.ibm.rqm.integration.service.IIntegrationService</url-pattern>
</web-resource-collection>