Anyone else experiencing the same issues after being upgraded to the latest version (10.0.603.0) of the platform? All my applications need a republishing. 

An application that is not re-published will give a "404". :-(

The warning message that show up for each app:

<AppName> has not been published since the last server upgrade. Please republish it to ensure its correct behavior. <AppName> has an outdated User Provider. <AppName> has outdated references. You should open the eSpace module, refresh its references, and then publish it. <AppName> uses References that have not been published since the last server upgrade.

Republishing the app in Service Center/Studio solves the issue. But this a heavy impact on other users if they are upgraded to this new version and experience the same effects. I see some core modules and themes are updated, but don't seem to be backwardscompatible...

Maybe this might also happening to Enterprise environments that are receiving this update...

Oh and btw, isn't there a way to republish all applications at once? Now it is just a time consuming (and annoying) task....

In order to republish everything: go to service center, solutions, and create a new solution. Add all components by using the *, and republish the running version of the solution. This will republish all your modules at once.

Regarding your other questions; I haven't upgraded any environment to 603 yet.

I upgraded from 9.1 to 10.0.6 and 10.0.7 in Linux, Jboss - Java stack.  Why is it that all my Solutions need to be republished each time I reboot?  I also have to run configuration tools each time I reboot!  How can I fix it?