Is there anything I can do to prevent my LTPA keys from becoming out of sync between my cells?

Yes. WebSphere Application Server V6.1 introduced a feature that enabled by default to automatically regenerate your LTPA keys. While this is a real nice feature for a simple cell configuration, any user who has multiple cells and requires that LTPA keys be in sync between the cells should turn off the auto-regen feature for LTPA. In WebSphere Application Server V7, this feature is off by default, and in for any new profiles that are created V6.1.0.23 this feature is turned off by default.