I had this problem in 3.4.x and 3.5.x versions of SQuirrel with the Oracle plugin and JDBC Thin drivers. I don't know if it's a problem with the OCI drivers.
The problem was introduced when I updated my driver jars from version 11.2.0.3 to 11.2.0.4.
Use the Oracle 11.2.0.3 jars, and the alias properties should work again.