It depends on how you have everything set up. If you're getting liferay's userIds in Alfresco, then it sounds like Alfresco might not be using CAS as its authentication source, otherwise I'm not sure how this could have broken in the way you describe.
I can provide some more detail on your problem, though. Before 4.3, Liferay stored its userIds as string usernames, usually autogenerated at user creation, such that a new user would either get the ID of ${company_Id}.$userIDnumber (i.e. the first user of an unconfigured liferay would be liferay.com.1), or an arbitrary sting you defined, like 'bob'. Coming into 4.3, liferay ended its dependence on the company_id value set in the web.xml, and moved to interger-only userIDs, and moved the string representaiton of a username into the 'screenName' ('screeName'?) field.
Based on your description, liferay is passing this userID value to Alfresco, which would have worked fine before Liferay 4.3. You need to find where this is happening and either tell liferay to pass the new field, or alfresco to request it, depending on your config.
