If "Hide CMD window Boot" control is ticked off, the path of the shortcut in the Startup menu of WinPE is wrong: "%SystemDrive%\Program Files\System32\Portable Finder CMD.cmd", hence it is not executed on boot.
Here are the lines from the log that are responsible for that because the third parameter of Add_Shortcut in the plugin is not specified:
Run - Processing section: [AddShortcut1Full] From file: [%BaseDir%\Projects\Gena\Basic\Build\Macro_Library.script]
[Parameter] with parameters: [AutoRun],[],[],[Portable Finder CMD],["%SystemRoot%\system32"]
...
[Success] IF - [] is equal to: [] evaluated string: [If,#3,Equal,,Set,#3,%PE_Programs%\%programFolder%\%programExe%]
[Success] SetVar - Sucessfuly changed the value of [#3] to: [%SystemDrive%\Program Files\System32\Portable Finder CMD.cmd]
The same Add_Shortcut line is used in "Portable Finder Startup" and "Portable Finder CD" plugins, but they have HideCMD_CheckBox control set to True and hidden.