Got it. I have reproduced the exact issue with Free commander.
The cause of the issue is the child process when executing Freecommander cannot be launched within the virtual bubble as it lies outside the ThinApp.
Here goes the fix that i have tried and worked for me. Add the below lines in package.ini of PS Hot Launch ThinApp under 'General Purpose Parameters'
ChildProcessEnvironmentDefault=Virtual
ChildProcessEnvironmentExceptions=FreeCommander.exe
Now rebuild the ThinApp by running build.bat. Delete any existing sandbox under %appdata%\thinstall before testing out the new EXE.
Please post your results.