That's quite some additional info.
For sure it creates some more possible causes.
First of all don't blame you to use such an app
But now it can be an issue with the app, Cross, the mediabase or any combination of these at certain moments/conditions.
If records end up 'dead' a common cause is 2 or more application trying to access at same time or while still being locked by an other app.
Could this be the case? e.g. Cross still open with these tracks loaded or recently used/selected (just before)?
Just maybe the app you use keeps (error)logs to register conflicts upon save.