Projects not showing up on Time Tracker

Are the items set as reportable?  By default all of the lowest level tasks in your projects are reportable.  For any other item (such as milestones) to show up on the timesheet, they would have to be marked as reportable.

Thanks for your quick response. The items that are actually showing up on the timesheet are milestones. I didn't do anything to mark the milestones for some projects as reportable and the milestones for other projects as non-reportable. How do I check to see if they're reportable (or change them if they're not)? Thanks.

Right click on the milestone, go to properties, then select the settings tab.  Reportable is a checkbox there.

One important note, only one hierarchical level can be reportable.  If you check this at the milestone level it will uncheck reportable on any tasks inside the milestone automatically.  I would also contact the person that created the project in order to determine which components should be reportable.

Thank you, that's what the problem was.

Is there any way to adjust the global settings so that for all projects we create, only the milestones are reportable, or would we need to manually change the settings for each milestone on every project? We're still in the process of setting up our system, but there's the possibility we may only want to track time at the milestone level.

This setting can be saved in your project templates, so every time you create a new project the milestones will automatically be set to reportable. Also, one shortcut is creating a custom view with the "Reportable" column so you can quickly set this without having to go into the properties of each milestone. I would also recommend hopping on any of our Q&A webinars to see this in action: 
http://www.clarizen.com/resources/online-demo.html#second

Thanks so much for your help!