Oops they have updated it again.. Yes check the boxes, cryptoprevent is a fire and forget programme it adjusts the registry so that known malware cannot run from its known launch folders. Check the programme monthly for updates by using the update checker within the programme
I would recommend disabling MSE :
Open the MSE GUI (doube-click tray icon or use the Start menu shortcut), select Settings , Real-time protection and deselect the Turn on real-time protection option.
OK for Java lets go the easy way :
Download Javara from here
http://singularlabs.com/software/javara/ the download link is on the right hand side
Run the programme and select update Java runtime
Once it is done then uninstall Javara
For malwarebytes run the programme and select Update and it will then download the latest