Message for upgrade to 4.0 version

Hi all,
My website was recentrly hacked, there were harmfull files added all over the worpdress installation (wp-admin,wp-includes). So I deleted all files and made a clean wordpress 4.0 installation.

After some days there was a message that was telling me to upgrade to 4.0 again. And I did, because I thought that maybe something went wrong or some kind of server changes were made and the wordpress version was not recognised propely.

Today I discovered a new malware file and deleted it. Now there’s a new message for upgrading to 4.0. What should I do?

Any suggestions?