pgAdmin 9.5 not showing all databases
I managed to find the problems.

One was I had an installed PostgreSQL server on my machine that I was unaware of. It seems I installed it with my pgAdmin install. So every time I connected to my server, I would establish a connection to my localhost server and not my remote server. I just uninstalled the server and installed only the pgAdmin client.



The second problem I had was that the file /etc/postgresql/9.5/main/pg_hba.conf had to be changed. So I ran:

sudo vi /etc/postgresql/9.5/main/pg_hba.conf


and changed the line

# Database administrative login by Unix domain socket
local    all    postgres    peer


to

# Database administrative login by Unix domain socket
local   all     postgres     md5


Once that was changed, I had two restart the configuration by executing:

sudo /etc/init.d/postgresql reload


I would also point out that it is important to have the postgres user as a unix and DB user with same passwords. I found all this information here.