What does Oracle XE perform during installation?
XE changes the following:


tnsnames.ora
Path variables
takes the default port 1521 for itself and this cannot be changed


The best way to install XE and other products is to install XE first, then any other Oracle version afterwards.

I think you can fix this by 


examining the path variables by entering PATH at the command line
ensuring that each installation has a file path to the bin folder, something like this

c:\oracle\db11g\product\11.1.0\db_1\bin;
c:\XE\product\11.1.0\db_1\bin;
check that the listener.ora has the correct parameters by starting a command line and entering lsnrctl status  This will show you which listener is in use, it's location and what databases it is servicing.
change the port for the non XE database to anything other than 1521 in the listener.ora