I've found this problem while using a Win7 Setup imgPTN from an ISO to install it under VBox.
1. Booted from my E2B UFD (1st partition FAT32) into E2B Main Menu.
2. Switched to my 2nd PTN (NTFS), where the Win7 Setup imgPTN (FAT32) was stored.
3. Booted the imgPTN and Windows Setup started. After entering required data I went away while Setup performed its job.
4. When I returned, I was expecting to find the CSM menu from my imgPTN. Contrary to that Windows Setup had already rebooted and was waiting for final user input before first logon.
5. After reaching Win7 desktop I rebooted to check what was happening with my USB boot, just find a bootmgr menu, where the 2 options were A) Just installed W7 and B) Boot to Windows Setup (the imgPTN in my USB). My CSM was gone.
6. Using the "Restore CSM/E2B" batch files in \e2b of imgPTN didn't help, no backup was found.
7. I recovered my CSM (and be able to switch to E2B Main Menu) by reinstalling grub4dos to UFD MBR with RMPrepUSB.
Seems like the problem is that Removable USB drives are seen as fixed when using "Virtual Machine USB Boot" tool. Win7 overwrote my UFD MBR and even edited the BCD in my \boot folder thinking it was a 2nd installed OS (although it was just the extracted contents of installation media), hence the bootmgr menu on boot.
I just hope this is not the behavior on real PC, where my UFD will be seen as removable.
Subject Win7 Setup imgPTN