Mail not working correctly after being opened by another App

So I first noticed this issue when I went to send some photos from Aperture, once I had hit send in the new message window the main screen of Mail appeared to be fine but I was unable to click on anything other than the menu bar, not only that, the message I had successfully sent was nowhere to be found in my sent box. It might be worth noting that I had first tried this after upgrading my MacBook with Crucial RAM and a Seagate Momentus XT HD. But since this I have tried everything:
First, I repaired disk permissions and checked all the preferences.
Second, seeing as I had previously recovered my old HD to my new one via Time Machine, and due to other issues, I though there might have been a corruption in the backup so I took the time to Clean install (where Lion was re-downloaded too), setup as new, and even create a new Aperture library.
Finally, I have reset the PRAM and attempted an Apple Hardware Test, which led me to another concern as on 3 occasions when starting up and holding down D it had a think about it but went to OS X and did not connect to the Apple servers for the AHT (as I have a Lion pre-installed Mac this should work?)
I have since checked out other things and have found that this issue also happens when sharing a contact from the Address Book but NOT when sharing a document from iWork. I have also noticed that Mail is still controllable from the keyboard when locked out from the mouse.
This isn't all I use my Mac for and isn't massively important but I'll be damned if I don't find out why only my Mac does this!
Please can anyone shed some more light onto what is causing this?
And why can't I perform a hardware test?

Hello,<br /><br />I am a newbie. I just created a Daily task report form in Adobe live cycle designer 8.0. I inserted a submit by email button in the form. In testing, i press the submit by email button, it is emailed to the specified person, however they are not able to see the form. Instead, a notepad file is sent with giberish info.<br /><br /><?xml version="1.0" encoding="UTF-8"?><br /><form1<br />><DepartmentName<br />/><ContactName<br />/><FromDate<br />/><ToDate<br />/><DateEntered<br />/><ProjectTask<br />/><Mon<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><ProjectTask<br />/><Mon<br />/><Tues<br />/><Comments<br />/><DropDownList1<br />/><CheckBox1<br />>0</CheckBox1<br />><CheckBox2<br />>0</CheckBox2<br />></form1<br />><br /><br />Can someone please assist me.<br />Thanks

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