I know this is a little old but I have a theory.
I am going to try reformatting the first (bootable) partition as fat32 before placing my boot loader and files on it again. Right now it is a large, bootable, NTFS partition, no separate boot partition. Bootmgr chainloads to Grub4dos. The same files work fine for all computers on an 8Gb fat32 USB flash drive. I also might try going with a small boot partition to mimic the flash drive. (I use RMPrepUSB for boot formatting.)
I have an external USB 3.0/2.0/eSata enclosure with a 250GB 3.5" HDD in it. I am connecting 3 PC's through their native 2.0 ports directly. It has 5 partitions, the first is 15GB booting Grub4dos rescue tools. This is normally successful!
Desktop -- Asus P8Z68-V, USB 3.0/2.0/eSata, Intel cpu, Win7x64 custom install
Netbook -- Acer AO722, USB 2.0, AMD cpu,Win7x64 OEM
Netbook -- Acer AOD260, USB 2.0, Intel cpu,Win7x86 custom install
The desktop loves the external enclosure no matter the connection, no matter the Bios settings. Boots right up. Both
of the Acer Netbooks hate it, while reacting to the flash drive just fine in either IDE or AHCI mode. Rarely, they both will detect the external HDD and boot to it, but most of the time they simply hang at post while the Bio (yes, Bios plural
) examine them and fail to detect anything. Leaving the other drive connected at the same time has no effect. Neither do Bio resets/cold-boots. (Originally, they both hung at post with the flash drive alone, until I let them boot a few times. Then the Bio made friends with it some how??? Not so much with the HDD.)
Oh, but they both detect the 3.0 flawlessly if I connect it while running Windows 7.
A second theory, the Acer's were not programmed to wait for drive spin-up on USB connections. On the rare occasions they detected the HDD the reboot was so fast that it had not had time to spin down (I can hear the noisy thing!) I might be SOL until Acer feels like fixing it.
Fortunately that was 2 of 2 theories, so I will be trying the fat32 reformatted boot partition tomorrow and report back. Hope all of this "intellectualizing" and "theorizing" ends up being useful to someone.