This seems like an issue similar to:
https://issues.jenkins-ci.org/browse/JENKINS-32996?jql=project%20%3D%20JENKINS%20AND%20component%20%3D%20teamconcert-plugin

Jenkins master is on Windows at 2.46.3, have Windows and Unix slaves, the slave.jars from this version are at version 3.7
The Team Concert Plugin is at 1.2.0.0
have configured the both 5.0.2 and 6.0.3 build toolkits in the Global Tool Configuration section.
The Jenkins master System configuration is using the 5.0.2 instance as the default tool, this is working for all slaves.

Am using a multi-configuration project in order to build on Windows and Unix platforms.

Have an existing team Concert Build took kit 5.0.2 defined in the Jenkins global configuration, with a Windows path defined there (as the Jenkins master is on Windows).
Each slave indicates to use the 5.0.2 team concert toolkit, and for all slaves, a new path for Unix and usually the same path for Windows, is given in the slave configuration. Builds are working on all platforms using the 5.0.2 build toolkit definition.

I wish to test using the new 6.0.3 Team Concert build toolkit, on only some slaves. I add a new 6.0.3 team concert tool configuration to the Jenkins Global Tool Configuration. As I wish to only test this version of the tool, I do NOT update the master configuration to make this 6.03 toolkit version the default, as I still have working builds (using the 5.0.2 toolkit) on other slaves).
I update only some of the slave connections I wish to test, to use the Team Concert 6 tool definition, and I update the slave configuration to name the Team Concert build tookit 6.0.3 , and the path to the Team Concert build toolkit 6.0.3 for that platform.

problem:

Normally, the log does not show which build toolkit is being used. Have opened this as a separate issue: (see: https://jazz.net/forum/questions/243295/how-to-tell-from-build-log-which-version-of-the-build-toolkit-is-being-used)

However, if I add the following environment variable, then I can see in the debug information which one is being used:

1. following to trace/debug/verify the Team Concert build toolkit (source fetch)
   com.ibm.team.build.debug=true

The logs show for Windows builds on the test slaves that are defined to override the 5.0.2 to 6.0.2 that the 5.0.2 team concert is being used .

For Unix, the builds are failing as it seems to attempt to concatenate the Unix slave root (/local/builds/pm/j4) with the (global) Team Concert 5 build toolkit location (C:\rtc\RTC-BuildSystem-Toolkit-Win-5.0.2\jazz\buildsystem\buildtoolkit) It is ignoring the team Concert 6 build tookit definition for the tool kit on all test platforms,.

(To get debugging for the Team Concert, I add the following to the environment: com.ibm.team.build.debug=true.)

Windows log:
....
Running remote true
buildToolkit property C:\rtc\RTC-BuildSystem-Toolkit-Win-5.0.2\jazz\buildsystem\buildtoolkit
Reusing facade for C:\rtc\RTC-BuildSystem-Toolkit-Win-5.0.2\jazz\buildsystem\buildtoolkit

Unix: Notice the Windows 5.0.2 path Jenkins master default location is concatenated to the Unix slave root (/local/builds/pm/j4)
Running remote true
buildToolkit property C:\rtc\RTC-BuildSystem-Toolkit-Win-5.0.2\jazz\buildsystem\buildtoolkit

FATAL: RTC : checkout failure: Built toolkit directory not found at: */local/builds/pm/j4/*C:\rtc\RTC-BuildSystem-Toolkit-Win-5.0.2\jazz\buildsystem\buildtoolkit

java.lang.IllegalArgumentException: Built toolkit directory not found at: /local/builds/pm/j4/C:\rtc\RTC-BuildSystem-Toolkit-Win-5.0.2\jazz\buildsystem\buildtoolkit

So, how can I test a new toolkit toolkit without overriding the master configuration?

When I set the Jenkins global configuration to use the Team Concert 6 toolkit, then every thing seems to work okay, but I should be able to test this toolkit without changing my master config.