It seems more of a server-side issue.
If the published applications were present before an upgrade, you could try set the icons again. (Start with some of them only to see if it helps.)
Otherwise, you could try to switch to standard resolution icons from the Site -> Settings -> Client Settings. (You may need to create a totally new connection on the client-side.)
If neither one of them helps, you will need to contact support as it does not look like a configuration issue.