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I forgot to say that I have checked and sql developer is point at the correct tnsnames file.
Can you please specify details about the failing connections?
Is there any more complex setup like cluster, SCAN-listener connection manager?
I was able to figure out what the problem was. In the directory were the tnsames.ora file is located there were some older files call for example tnsnames.sav or tnsname.old once I removed all files except the file called tnsnames.ora the connections worked without a issue. There is a note called How SQL Developer Determines Which Tnsnames.ora File to Use with Multi-Oracle Home Presence? (Doc ID 566428.1). but after reading that since I running Version 3.1 of Sql Developer and I used the option to specify the location of the tnsnames.ora file should have overriden any other option. However, until I removed from the directory all files starting with tnsnames and just left the single file tnsnames.ora I was getting the error. The give away was that I had four entries for each entry in the tnsnames.ora file but guess what I had four file in the directory starting with tnsnames.