Why is Lion installed on external HDD and iMac says that Lion is already installed when it is not?

I went into the Apps store then logged in to confirm that I wish to pay for the Lion upgrade from Mac OSX v10.6.8.
The downloaded 3Gb installation file went into my Applications folder after a few hours:
This installation application is still in the Application folder of the iMac.
During the upgrade / installation, I got the following message, saying that the installation can't go in the HDD of the computer I was working on (ie. the iMac's Macintosh HD). I had no choice but to select the external HDD (WD-1T) as the installation destination, which proceeded very quickly.
When the installation was complete, the iMac rebooted into a fresh Lion installation, running off the WD-1T! I can see all my old files on the Macintosh HD, as if that HDD was the external HDD!
If I disconnect the WD-1T upon rebooting, I am back to Snow Leopard, running from the iMac's Macintosh HD. If I go the App store, it tells me I have already installed Lion on the iMac (when it is not the case)!
When I go to my MacBook Pro (currently on Snow Leopard and not part of from the above installation), I see that Lion is purchased but not installed. If I click INSTALL, it starts to download what the iMac had earlier downloaded (the Install Mac OS X Lion.app is still sitting in the Application folder of the iMac).
Question:
Can anyone shed some light why this happening and how to get Lion onto the iMac?
How to install Lion on the MacBook Pro without re-downloading the software?

I would say it is related to the purchase date. FaceTime is included in 10.6.6~8 OEM discs.

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