When translating a command-line for windows, one extra set of quotes gets added which prevents the execution of the command. I raised the log level and got the following example:

Configured command-line:
tools/ci-build_continuous_debug

This gets converted by hudson.util.ArgumentListBuilder.toWindowsCommand(). The log output is created by calling ...toStringWithQuote():
cmd.exe /C ""tools\ci-build_continuous_debug && exit %%ERRORLEVEL%%""

After feeding this into a hudson.Launcher instance, the jobs console log shows:
cmd.exe /C '"tools\ci-build_continuous_debug && exit %%ERRORLEVEL%%"'

When manually entering the command, the correct string is:
cmd.exe /C "tools\ci-build_continuous_debug && exit %%ERRORLEVEL%%"

I don't know if this is important or not, but this happens with a slave running on Windows while the Jenkins server is running on Linux.