I think you may have configured Grub4dos menu, to have a entry for the install to the internal drive and also, a entry to boot the install, on the USB.
It will do that, unless you tell it to configure, only for a specific drive.
Do this, so the menu entry, when booting from the internal drive, is only for installs, on the internal drive.
Boot the computer and do not have the USB plugged in.
This for sure, makes the only thing running, is what is on the internal drive.
Look on the desktop, at the drive icons, showing lower left side.
All should be sda something.
Run the Grub4dos Bootloader Config
Select the sda drive as location, to install boot loader.
Select search within only this device
No other selections, need to be done.
Keep selecting OK, until program completes.
Now when you boot, from the internal drive.
The only boot menu entries, are for what is on the internal drive.
Note:
1st menu entry is usually the normal boot mode.