When you run the portable version, the "start with windows" is not applyied to windows, because in "portable mode", BPM doesn't store any setting in windows.
It's the goal of portable version: no trace left on the system, when running from a USB key for exemple.
So, in "normal mode", the "start minimized" option store a parameter in windows registry, and this option is not stored in "portable mode", its a feature.
If you want to run BPM minimized, it's possible!
Just create a shortcut to ProcessManager.exe, and add the parameter "-minimized" the the path to exe line.
Ask for more informations if needed.
Rubik's Addicted !