Since Liferay Portal v4.1.2 the ids of portlets and themes are manipulated before writting them to the database. In particular all characters that are not safe to be used in JavaScript scripts (spaces and minus signs) are removed. Liferay 4.1.3 and Liferay 4.2.0 include an upgrade script that modifies the database to mantain change any old portlet or theme reference to conform to the new naming convention.

While the upgrade script should cover 99% of the situations there is a 1% that is not covered and you should be aware of. If you are using custom layout templates that define columns whose names are not of the form column-N where N is a number from 1 to 10 then you should upgrade the portlets referenced from those columns yourself.

In order to do so review the typePreferences of entries of the Layout_ table that use the non-conforming layout template and edit it's contents. You should keep the properties-like format and only change the portlet ids to remove the spaces and minus signs in the cases where they are used.