Two Version of Windchill on Same Machine

I agree with @avillanueva.  It sounds like maybe wt_home is set in the OS environment variables.  This response is Windows centric, but the same concepts apply to Linux.

The two installations need to be fully independent.  So...

• Choose a DB release that is supported by both Windchill versions.
• Don't install Java with the operating system because multiple releases have multiple unique Java requirements.  Extract the zipped Java bundle to the Windchill load point and give it a generic name: D:\PTC\Windchill_12.1\Java.
• Ensure the Windchill variables are not set in the OS.  Set your environment variables in the properties and batch files that launch and run Windchill.

The Windchill shell shortcut created by PTC doesn't use any variables.

Target: D:\PTC\Windchill_12.1\Windchill\bin\windchill.exe -w "D:\PTC\Windchill_12.1\Windchill" --java="D:\PTC\Windchill_12.1\Java\bin\java.exe" shell
Source: D:\PTC\Windchill_12.1\Windchill

If you are running a CMD shell and launching the shell environment, ensure you are in the correct load point.

pushd D:\PTC\Windchill_12.1\Windchill\bin

windchill shell

Other thoughts....

folder mappings

The old PTC demo images used drive substitution/folder mappings to replace content associated to a common software load point.  For instance, we want the Windchill load point to consistently be D:\PTC\Windchill_12.1, but we have two installs: E:\12.1.1.2\PTC\Windchill_12.1 and E:\12.1.2.4\PTC\Windchill_12.1.

:: Remove mapping

subst d: /D

:: Create mapping

subst d: E:\12.1.1.2

This technique really isn't necessary unless you want a common load point (D:\PTC\Windchill_12.1) and both installs are different builds of the same major.minor version (12.1.x.x).  I mention this only in case you are using drive substitution/folder mappings and maybe forgot to switch the mapping before attempting to launch the second version.

Windows Services

On Windows, even in development images, I register Windchill and Apache as Windows services and set them to manual launch.  Then I use a batch file to start the appropriate services for the version I want to launch.

net start 12.1HTTPServer

net start 12.1Windchill

On Linux, many companies use a bash script registered through .bashrc to do the same start/stop commands via command line.

Named Java Processes

Naming the Windchill processes helps to quickly identify which version is running, what process is doing something, or what process(es) crashed.

xcopy /y %java_home%\bin\java.exe %java_home%\bin\java_sm_121.exe 

xcopy /y %java_home%\bin\java.exe %java_home%\bin\java_ms_121.exe 

xcopy /y %java_home%\bin\java.exe %java_home%\bin\java_bgms_121.exe 

and in Site.xconf...
<!-- Named Processes -->
<Property name="wt.manager.cmd.BackgroundMethodServer.java.cmd.quoted" overridable="true"
targetFile="codebase/wt.properties"
value="$(wt.jdk)\bin\java_121_bgms.exe"/>
<Property name="wt.manager.cmd.MethodServer.java.cmd.quoted" overridable="true"
targetFile="codebase/wt.properties"
value="$(wt.jdk)\bin\java_121_ms.exe"/>
<Property name="wt.manager.cmd.ServerManager.java.cmd.quoted" overridable="true"
targetFile="codebase/wt.properties"
value="$(wt.jdk)\bin\java_121_sm.exe"/>

Just some ideas.