Since your site is producing a phrase message that doesn't actually correspond to the 4.1.x contents of the files that generate this error, it is possible that your PHP is still running 4.0.26 versions of the files that it has stored in memory.
If your site is using an opcode cache, such as PHP's built-in cache, and it has long-lived or no expiration, then you may need to restart PHP in order to pick up the changes to your file system. Otherwise PHP may continue run your 4.0.26 upgrade files, which do not represent any changes from 4.1.x, and which would load configs and files at a path which does not even contain 4.1.x files.
If this is what your setup requires, you MUST remember to perform this step whenever you make any changes to your site's software, or it can cause errors that don't make any sense, or damage your database.