When starting any executable from inside FreeCommander the executable should be normally provided with the current directory, from where the executable was actually called. In build 744 (or maybe already 743) FreeCommander sets the "current path" for calling the executable always to the folder where FreeCommander.exe is located, not the executable being called.
Repro:
Create a batch file test.bat to display the current directory:
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@echo off
echo %cd%
pause
Open test.bat either by double click or Enter key from FreeCommander.
When doing this from build 742 you will get:
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C:\Temp
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C:\Program Files\FreeCommander XE