If you configure log shipping on a clustered instance where the program files is something other than the main system drive, log shipping stops working once the instance is failed over to another node. The reason is that when the Add Node operation is run on the other node(s), it does not configure the SQL Server instance properly. On the original node, everything is installed properly (for example, Z:\Program Files\Microsoft SQL Server\100\Tools\Binn\SqlLogShip.exe). On the other node, it puts SqlLogShip.exe on the original system drive. The SQL Server Agent job LSBackup_DBName references this as its step:
"Z:\Program Files\Microsoft SQL Server\100\Tools\Binn\sqllogship.exe" -Backup 6B81BF42-4AA8-4DE3-8349-5E54EE0C52ED -server KILROY
So clearly this will not work when things are failed over to another node if SqlLogShip is not where SQL Server is expecting it to be.
See pictures for verification and also check my blog for integrated pics and instructions.