Tested and confirmed on the default 10.1.0.3 installation and I'm pretty sure I've seen it on at least 188.8.131.52.
If the directory /var/opt/oracle exists during the Oracle installation the dbhome script will have the parameter ORATAB set to "/var/opt/oracle/oratab" instead of "/etc/oratab". The normal DBCA process during a default installation will still add the instance entry to /etc/oratab.
This causes the oraenv script to fail finding the ORACLE_HOME and will prompt the user. oraenv calls dbhome to determine the ORACLE_HOME for the instance selected.
Modify the dbhome script(s) in your "common" path (usually /usr/local/bin) and in $ORACLE_HOME/bin.
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I'll submit the TAR to Oracle and see what they say about it. Tiny bug, I'm quite sure that not many people create /var/opt/oracle on Linux.