CS5 HDR pro two photos alignment issue

Although I really enjoy the new tool, I'm having trouble aligning two photograph when I open then through the HDR pro tool.
Why is alignment of two photos so bad in HDR pro and perfect if you align the two same photos as two layers? I've even tried reopening the same files over and over and get different results each time in HDR pro.
In view of this, shouldn't there be a realign button in the slider adjustment screen, or options for alignment, such as Use the regular auto-align?
Since alignment works fine with layers, is it possible to have an option to use layers as a starting point for HDR pro instead of opening saved photos only? I realize this probably might not give perfect results as just fixing the automatic alignment issue...
But hey, I'm just trying to find a workflow around this if I didn't have my tripod with me at time of shoot... and I shot only two photos to composite.

Hi Chris,
thanks for looking into this matter. Where do you want me to send the files (over 50 megs zipped).. they're CR2 files...
Date: Fri, 28 May 2010 14:38:51 -0600
From: [email protected]
To: [email protected]
Subject: CS5 HDR pro two photos alignment issue
Don't know what could be going wrong.  Can we get the files so we can try to reproduce the problem here at Adobe?
>

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