Key commands not working

I found an old post about this, but it didn't seem to have a solution to the problem.
Some key commands I assign simply don't work. They even show up in the menus, but don't do anything (one example, I tried assigning shift-m for Create Marker without Rounding).
Also, when the key command window is open, typing some key commands jumps to the assigned command, but with others it doesn't (I can see one of the menus at the top flash, as if it's trying to actually do the command). One example of this is command-m which is assigned to open movie. (oddly, getting rid of open movie and changing command M to create marker without rounding worked, although it still didn't jump to it in the list)
If the function to show used key commands isn't working, how am I supposed to know what's free for additional key commands?
I'm using the standard US keyboard, standard key commands in tiger (which don't seem to overlap any of the ones I'm tweaking).
Any ideas on this? It's very frustrating and a big waste of time.

It's also a pain that the key command window shows codes for the keys instead of what the keys actually are. <<</div>
Actually, there are 2 methods for simultaneously assigning/viewing the assignment; one shows you alphanumeric charaters and one shows the key codes. But it is true that some key assignments won't work unless they're assigned as key codes.
I agree -- it's time to either revamp this window (with all of the features you mentioned) or offer an explanation as to how it actually works so that people like us aren't left pulling our hair our because this window's functions don't always seems to work properly. Something like:
"Hi, this is the Apple/Logic guys. We realize that some users find the Key Commands window to be problematic. Well..."
and then it could go on in some of the following ways...
a) there are a few things that don't work properly, such as X/Y/Z... We're hoping to fix the problem in the next release of Logic..."
or
b) if you're trying to assign (whatever) to (a function) and it doesn't work, try this instead...
or
c) if you're trying to assign (whatever) to (a function) and it doesn't work, please know there's an issue with this particular aspect of the Key Commands window that will be fixed in a future release...
That's the kind of thing I think we'd all love to see.
Maybe that's enough venting for now. Wouldn't want to attract the attention of the "venting police" LOL

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Below is a copy of a bug report I just submitted to Adobe. I don't suppose any users have run across this and found a solution or workaround?
I found someone else with this problem in an archived topic thread, but the only response that poor fellow got was an accusation of not following instructions (His problem wasn't user error, BTW).
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******BUG******
Concise problem statement:
Modifer keys do not work with mouse: For example, free transform or rotate behaviors that require "Click-Ctrl" .
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Expected results: The cursor should change shape as the ctrl key is pressed and the object should distort rather than scale.
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Primarily using Wacom Intuos3 tablet. (with latest drivers), but have also tried combinations with microsoft mouse or both mice installed.
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Thanks Guys,
Good to know it's working for you. I guess that's the nature of intermittent bugs. Of course, Adobe's bug report form has a field for version, which I, of course, filled in. Sorry I didn't add it to this post. I'm using the latest version CS3 v13.0.2.
Stephen,
Sorry I was not more clear when I said, "For example, ...". I was talking about the modifier keys not working with several different tools. The Free Transform tool advertises functionality that is supposed to work with a "Click (down, but don't release)then hold down Ctrl" combination. The Rotate tool advertises a behavior that is supposed to work with an "Alt-Click" combination. These are just 2 examples of the modifier keys not working. I focused primarily on one example in the bug report(ctrl after and in addition to click in the free transform tool, not alt-click in the rotate tool).
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(From the "Distort Objects with the Free transform tool" help topic)
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Start dragging a corner handle on the bounding box (not a side handle), and then do one of the following:
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To rotate around the center point, choose Object > Transform > Rotate, or double-click the Rotate tool.
To rotate around a different reference point, select the Rotate tool. Then Alt‑click (Windows) or Option‑click (Mac OS) where you want the reference point to be in the document window.
Enter the rotation angle in the Angle text box...."
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Thanks Again

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My illustrator CS6 short commands have stopped working.
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Date: Wed, 8 Jan 2014 15:39:58 -0800
From: [email protected]
To: [email protected]
Subject: Illustrator Short Commands Not Working
    Re: Illustrator Short Commands Not Working
    created by Jacob Bugge in Illustrator - View the full discussion
THS,
You may try the following (you have tried/done some of them already) and see whether it helps (the following is a general list of things you may try when the issue is not in a specific file; 3) and 4) are specifically aimed at possibly corrupt preferences):
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http://www.adobe.com/support/contact/cscleanertool.html
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Few keyboard keys are not working

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Yesterday, when i made my laptop shut down, all the keys were working perefectly.
Even when i started it today, for few minutes ie 5 minutes all the keys were working fine, But then i don't what happned suddenly.
Pointer starts blinking.. Down arrow key was getting pressed itself.
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