I'm now running 10.8.4 on new hardware and still getting the same issue.
The bug affects Graphic Converter and Acorn, basically anything that uses the OSX colour picker.
Drewmweaver which has its own colour picker (does not use the OSX picker at all) is not affected.
Things that seem to make a difference:
** Rebooting the Mac completely
** In the WaffleSoft Hex color Picker untick the option for "Dont generate calibrated colours"
Graphic Converter will usually select the correct hex number, but once you OK to close the picker and return to actually using the color it will silently change - if you reopen the picker you will see that one digit of the hex code is different. In my tests it always seems to be a shade darker
Acorn will usually select the correct hex number, but once you close the picker it will also change the colour. In my tests it drew a slightly lighter shade.
In the WaffleSoft Hex color Picker tick the option for "Don't generate calibrated colours"
Select the colour - this will give you the right Hex code - copy it to the clipboard
Now untick the option for "Dont generate calibrated colours" - this will change the hex code slightly
Now Paste in the first hex colour - the pickers sample swatch will look wrong
Press OK and draw in Graphic converter - the colour will come out right
The Apple DigitalColorMeter can also be used to select the correct Colour code but you will have to convert the RGB number to hex and then copy/paste into the drawing program.
The Colours App (http://mattpatenaude.com/) selects colour codes that are the equivalent of having "Don't generate calibrated colours" ticked.
This bug doesnt seem to be in the Color pickers ability to select the right colour (or have anything to do with colour space) but something about the way the value is returned to the calling application.
Another year later, this problem still exists with the Colour picker and Graphic Convertor.
I switched to Pixelmator and that seems to be OK, they recommend switching to the sRGB display profile in System Preferences/Displays and now I can use the colour picker to select colours (eg from http://www.color-hex.com/ ) and Pixelmator will insert the right colour into an image.
If I go back to Graphic Converter with the same profile selected and an image with the profile sRGB specifically selected, the colour picker will select the right number but when added to the image the colour is still wrong.
So it seems that Adobe fireworks and Graphic Converter are both unable to work with the OSX colour picker but Adobe Dreamweaver and Pixelmator manage to get it right.
You are wasting your money if you buy new hardware in an effort to fix this issue. The problem is that the Apple Color Picker is influenced by the monitor's color profile. I do web development on a Mac Pro with 3 monitors and I get a different result from the color picker when I sample the same color on each monitor. It's quite frustrating.
The only solution that has worked for me is setting my monitors (and the color picker color profile) to sRGB IEC61966-2.1.
*****You must change the color profile in "both" your monitor settings and in the color picker or it will not work.******
An easy way to test if the color picker is returning the correct colors values is to sample any color on your screen and then sample again from the results in the picker. It the colors change when it samples from it's own swatch then you know you still have a problem.
It's a crappy solution to the problem because you are then working on an uncalibrated display, which is not very conducive for producing professional graphics. A few years ago I was using a color picker that would ignore the monitor profiles and give me the correct values. With the newer versions of the Mac OS it no longer works.