I don't have Win98 anywhere anymore... but I'm 70-80% sure that I had CF 5.0 set up on Win98 a while back and the scheduler was working fine.
Don't quote me on it, though. And I'm more sure that it wasn't SE... so maybe it's a moot point.
However, I'm fairly certain that, if it didn't work, you'd see a lot of bug reports and knowledgebase entries about it over on macromedia.com.
Are you using "CFSCHEDULE"? Or entering the task directly into CF Administrator?
-Carl