So I see this problem was from 2012, and here it still exists in 2014 as I just loaded CS6 and have the exact problem. So just in case anyone else needs a fix/workaround, here's what I did to overcome this problem in Windows 7.
The problem is that the registry settings for Dreamweaver are getting reset to FALSE.
So I first set up Dreamweaver how I want the code view to be, then exit Dreamweaver.
Next, backup these good registry settings by launching regedit.
Disclaimer: If you are not familiar with manually editing the registry, please know that making a mistake in the registry can seriously ruin your day.
So tread carefully and be sure to backup your registry before making any changes, and you should also have a full backup of your entire system drive, but that's a whole other topic).
To launch regedit, go to Start > and type regedit in the search box. Or you can open a command prompt and type regedit from there.
The key is that you need to launch regedit as the same user who is running Dreamweaver. In other words, don't run regedit as Administrator. Because we need to edit settings that will only display as the Current User.
So with regedit open, navigate to [HKEY_CURRENT_USER\Software\Adobe\Dreamweaver CS6\FloaterStates]
You should see settings that have the same name as the settings sat in Dreamweaver's code panel (Auto Indent, Line Numbers, Syntax Coloring, etc).
Notice their Data Values, TRUE and FALSE as they were set in Dreamweaver.
So what we need is a .reg file with just these settings, set as we want them to be. And then we can run this .reg file to set the settings as they should be before launching Dreamweaver each time.
The following lines between the ///// marks are the contents of my .reg file with the settings as I want them...
//////////
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Adobe\Dreamweaver CS6\FloaterStates]
"Wrap"="TRUE"
"Line Numbers"="TRUE"
"Syntax Coloring"="TRUE"
"Auto Indent"="FALSE"
"Highlight Invalid HTML"="TRUE"
"Hidden Characters"="FALSE"
"InvalidHTMLHighlighted"="TRUE"
////////////
Save your settings in a file called something like dreamweaverCS6ViewFix.reg
So now, if you run this .reg file by double-clicking it just before launching Dreamweaver each time, your code view settings will be correct, and you can get to work.
I did one more step which was to create a .bat file with automatically runs this file, then launches Dreamweaver. But it opens up another command shell which some people may find annoying.
But I just close it out and all is well.
If interested in doing this, create the .reg file as above, then create a .bat file to launch it plus Dreamweaver.
Here's the contents of the .bat file, between the /////
Note the :: marks are comments in the DOS script.
Change the file paths to what they need to be on your system. This works on both CS5.5 and CS6, changing the paths in registry and file path respectively.
If you run into any problems like this and can't figure out my post here, let me know and I can try to help.
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:: DOS script to run a reg file to fix Dreamweaver code window settings before launching Dreamweaver.
:: Written by Brian Hoard, www.BrianHoard.com
:: It's the only way I could figure out how to keep the settings from resetting.
regedit /s c:\YourDirectory\dreamweaverViewFix.reg
"C:\Program Files (x86)\Adobe\Adobe Dreamweaver CS6\Dreamweaver.exe"
exit 0
//////////