Win 7 reinstall issue?

I originally installed WIN 7 onto an eide 250gb drive (upgrade from XP) and all went reasonably well. It's a multi-boot configuration and I used EasyBCD to add the second and third systems (win install image and Ubuntu Linux).
I bought a new 500gb SATA II hd and reinstalled WIN 7 - because I couldn't find an acceptable method of moving the WIN 7 over to the larger drive and didn't want to spend more money on questionable "cloning software" as I've made that mistake before. So, I reinstalled WIN 7 onto the 500gb drive. What I was surprised to discover was that when the install rebooted, it had my multi-system configuration with the new WIN 7 at the top. OK, I thought and let it finish. I used Easy Transfer (somewhat disappointed with that app as it didn't pick up my programs) on the old and new WIN 7's and all was cool. I renamed the new WIN 7 via EasyBCD to WIN 7 SATA to distinguish it from the other...both boot fine (haven't tried linux yet, but I have no reason to believe it won't boot). I decided to try booting directly from the 500gb SATA drive, so when my system restarted I selected the boot menu, hard drives and then the SATA drive. I was a bit surprised to find it wouldn't boot! I'm troubled by this because it was/is my goal to eventually use the original 250gb drive for backups and general storage, but if I wipe it, it would appear I wouldn't have a bootable system anymore.
Does anyone have any ideas about:
1.) why the second install used the original BCD?
2.) how to I "fix" it so the second hdd will boot, without having to disable the
first hdd and perform a "system repair" via the install disk?
Thanks.

Because you own a WD HD you are entitled to use superior Acronis free version downloadable from the WD Support Downloads webpage for your model HD.

The best way to multi-boot when you have separate HD's is via the BIOS boot order or one-time BIOS Boot Menu key given on first boot screen. This keeps the HD's independent for hot plugging or to come and go as you please, whereas Windows-managed Dual Boot interlocks them. This is especially important when you have Linux involved as GRUB will corrupt your Win7 installs.

Please post back a Win7 Disk Management screenshot with all drives plugged in using Snipping Tool in Start menu. Tell us what is on each drive, and we'll give you the steps to recover the MBR into your new Win7 partition so you can boot it via BIOS, then you can use EasyBCD to Edit OS menu to delete listings and boot the other Win7 also via BIOS until you are ready to get rid of it.

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