I recently cloned my HDD to an SSD using Clonezilla. Now if I try to boot from the SSD it gets stuck on a black screen with a blinking cursor. But if boot into Hiren's BootCD and use the "Boot Vista/Win 7 (BOOTMGR) from hard drive" option it boots from the SSD and loads Windows just fine (I'm writing this post from within Windows booted from the SDD in question).
I've tried using my Windows 7 dvd to do a startup repair, it reports no problems. I thought maybe it was UEFI/SecureBoot, but disabling that in the BIOS seemed to make no difference.
It's mot likely the missing boot manager. You have to clone the os partition and the 100mb system reserved partition at the beginning of the hdd.
I don't think the HDD had a system reserved partition. Clonezilla didn't see one, the Computer Management tool in Windows doesn't see one...
Computer Managment lists my SSD single partition as "System, Boot, Active, Crash Dump, Primary Partition". The only partition on the HDD is now listed as "Active, Primary Partition".
Edit: Update. I tried using MBR Regenerator. After a reboot, now it says "A disk read error occurred" instead of just showing a flashing cursor when trying to boot directly from the SSD. I can still boot successfully using Hiren's BootCD.
Update 2: Turns out the problem was Clonezilla. I started the process again, this time using Macrium Reflect, and it worked perfectly. Didn't even have to do a boot repair, it just booted right into Windows first time. And it did the clone right from inside the Windows that it was cloning. Mind. Blown.