Ok, reported bugs have been fixed, and the variables have been split into the 2 files. I will be bug testing tonight and part of tommorow to track down anything that slipped by and then 4.1 will be available to registered users. Because of the theme change, this is a full upgrade that affects every file in the package, so those that are running 4.0.1 will need to update all files.
This should not be a regular upgrade process. Most upgrades will allow you to only replace the files that have changed, and in most cases this shouldn't be every file. I know it is a pain to upgrade for those that have made substantial changes to the program and I will try to keep the full upgrades to a minimum.. The database has not changed at all, so there will be no altertable to run.
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Scream
http://www.screamingweb.com