Failed boot with flashing folder, but boots from USB

Hi,
I was recently running an app from the App Store, when my computer froze. I got the classic spinning beach ball on the app, so went to the dock to ctrl-click the dock application icon to force quit it. This then crashed my dock. After some time I gave up, and force-turned my MacBook Pro (13-inch, Mid 2009) off by pressing and holding the power button.
I turned my mac on again, booted to a gray screen, then 30 seconds later a folder with a question mark in it began flashing on the screen.
My Mac did not progress further in its boot. So I did all the usual stuff;
I re-installed my RAM and HDD (both of which I have upgraded a little while ago to improve specs) and tried to boot again without success.
I tried to access the recovery partition by holding alt while booting, to no avail, doing so just left me with a grey screen and a mouse pointer displayed. I believe that this may have been the case because I boot from an encrypted hard drive (I have encrypted it using filevault) and I have heard that recovery mode is inaccessible when booting from an encrypted drive.
I zapped my PRAM. (cmd-alt-P-R)
I tried booting into safe mode. (⇧)
Nothing worked. I then, as a last resort, removed the HD from my MacBook Pro, and swapped it with the non-encrypted drive that I use to back up menial data. I tried booting from the unencrypted drive into recovery mode, and it didn't work.
However this is the interesting bit. I then tried to boot (via USB) from the encrypted (original) HD that I had put in my external enclosure. This works. I logged in (past the encryption) and can now use my computer as normal.
I would therefore think that my Mac has something wrong with the HD bridge, or the HD cable inside my Mac. However, I can now read from and right to the unencrypted HD that I installed in my mac!? Very Wierd!?
If anyone has any ideas about what may be going on, I would be very gratefull, as I can now only boot my Mac via USB, which is a hastle to say the least. I include a screenshot.
Thanks so much!!
Mr BlobE
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In this case sig the interesting thing is that the computer boots when the Startup Disk is connected via USB. In other words, my laptop will read and write, but not boot from the internal drive. Thanks Linc Davis, I have done just that and should hopefully have a working mac by tomorrow!