Just a theory while I wait around on the current install attempt
At the hard drive selection point of Windows 7 setup, I am noticing that the flash drive is marked as having a "System" partition on it. This strikes me as a bit odd... is this normal behaviour for burning the RC1 ISO to a flash drive?
Unfortunately I cannot remember which thread I read it in, but someone mentioned that if setup sees an existing System partition, it will put the boot information and all the rest inside it (which means it won't do the "Windows might create additional partitions..." prompt). Hence why BOOTMGR is ending up on the flash drive, not the main hard drive.
Anyhow... I'll post a screenshot of the partition list once this setup finishes
Thanks for the replies so far.
EDIT: Okay, here it is. As you can see, there's no sign at all of the "System Reserved" partition. Just to be ultra-clear:
* Disk 0 is the Windows 7 setup flash drive, connected by eSATA. If I unplug it and try to reboot, the old "DISK BOOT FAILURE" message appears.
* Disk 1 is the main hard disk, split into a 30Gb chunk for Windows to live in, and the rest for general files and whatnot.