There is a bug in the latest release (build 2279) - the Scheduler doesn't clear the previously used CSS classes.
It should be fixed in the latest sandbox build (2306):
http://javascript.daypilot.org/sandbox/scheduler/
I've tested this dp.message() call in the console and it seems to work fine:
dp.message("Test", {delay:5000, cssClass: "custom_message"});
Let me know if the problem persists.