Projects above the Waterline on the Waterlines tab are not showing as above waterline on the Capacity tab's Investment Schedule portlet.
You have to filter on All projects or "Above Waterline = No" to see them.
I tried running the ranking rules and also syncing the portfolio.
Environment
Release : All Supported Releases
Component : CA PPM SAAS PORTFOLIO MANAGEMENT
Cause
This can happen if there are pending changes on the Waterline tab that haven't been saved after manually modifying the waterline (by dragging and drop)
Resolution
1. Go to the Waterlines tab in the Portfolio 2. Click the Save button
Highlighted in yellow below is the Save icon on the Waterlines tab.
If the icon next to it (Discard Changes) is enabled, then that means there's a change pending being saved.
Additional Information
See KB: 141061 for tips on how to optimize use of Self Service for Clarity PPM