EJBs packaged in a WAR are using the web / lite profile of EE6. As far as I know, timers and some other features are not supported in this profile. So if you want to use timers you would have to package your ejbs in the traditional ejbjar + war + ear way.
I could not find a reference for the web profile, this is the closest to a comparison: http://www.theserverside.com/news/1321142/Part-Three-New-Features-in-EJB-31
Edit: I stand corrected, war packaging is actually described in jsr 318, EJB 3.1. Since I could not find any restrictions on available features in that section of the spec, timers should also work in an ejb packaged in a war.
