Rectangular selection quirk and file saving bug

I am trying to figure out a way to select areas and create a new image file using this selection using either the selection tool or the slicing tool so that transparent pixels that extend around the object that I am selectly are included in my selection. But Photoshop in it's brilliance changes the selection area to only include the non-transparent pixels. I realize that this might be useful sometimes, but by default I would expect if make a selection that I want, I get the selection that I want (like other similar programs that I have used). Is there are way to dumb-up Photoshop so that it just does what I want or at least a clever way to out-smart Photoshop (I'm using CS5).
Also, I am also one of the lucky ones that has problems saving files, with Photoshop indicating that that particular file is "already in use or was left open by another application".  I didn't seem to have this problem when I originally got CS4 and was running Windows XP. But since upgrading to Windows 7 it happens all the time and it is getting very, very annoying.  Has anyone heard of any new workarounds for this problem? One of the reasons I upgraded to CS5 from CS4 is that I was lead to believe by Adobe that CS5 would fix this problem. Well it didn't and it is getting progressively worse.

Let me make sure I understand this, you want to start with one image and create another that has only some parts remaining, with the rest being transparent, right?  The key is that you want to keep the exact same canvas size, right?
About a year ago someone on here asked if an action could be made to do something just about like what you're asking.  As I recall, I tossed together an action that worked to do the job.  You might try searching this forum site for that.
Actually, you may not have to search...  It looks like I left a copy on my site in the folder I use to share things:
http://Noel.ProDigitalSoftware.com/temp/New_Document_From_Layer_3.zip
+1 for Mylenium's suggestion that something you've installed or configured is getting in the way of Photoshop's file access.  It simply doesn't do that on most other Windows 7 systems.  What security software are you running?  Antivirus/antimalware software absolutely should NOT be interfering with your normal operations.  If it is, it needs to be removed and a better brand needs to be installed.  I personally prefer Avast Internet Security and have never had it interfere with computer operations one iota.
You can also disable indexing and turn off the generation of Thumbs.db files in Windows 7.  Both of these things could help and have virtually no downsides.  Let me know if that's something you want to try and I'll turn up the instructions on how to do so.  They're also here on this forum somewhere.
-Noel

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