I've been trying to install applications, web pro explorer, juke, etc... and receive an error.

Attached is my log, help.

You need to update the system first before the new apps can be loaded.
Open tools->settings->check for updates and then update your Tonido System first.
Then the system will restart and your apps will now load.

Its states that all services are up to date. I ran the check for udpates and it states the same. When I go to 'Activate' an app, I get the "Failed Applcation Action! Failed loading Application: The application could be incompatible. Check if there is a newer version.

Please download and install the Tonido Desktop software from our website and just do an install. It will fix the issue.

Do I have to be concerned about any files being overwritten if they are going to the same directory?

You can make a backup of the C:\Documents and Settings\charock\Application Data\Tonido\data folder.