As near as I can tell, the nib has gotten corrupted somehow, or perhaps there 
is some setting that you were previously able to set in IB that is no longer 
exposed, or is really non-obvious.

To fix, you can simply recreate that cell in the matrix or, if you're not 
squeamish about manually editing the nib file, you can do what I did.

I opened the nib in BBEdit and found, in designable.nib, where the three cells 
in that matrix are specified. It looks like this:

<int key="NSCellFlags">68157504</int>
<int key="NSCellFlags2">132096</int>
<string key="NSContents">Permute Locations</string>
...
<int key="NSCellFlags">1141899328</int>
<int key="NSCellFlags2">140288</int>
<string key="NSContents">Permute Genes</string>
...
<int key="NSCellFlags">68157504</int>
<int key="NSCellFlags2">132096</int>
<string key="NSContents">Permute Individuals</string>

Note the NSCellFlags and NSCellFlags2 are different for the middle cell. I 
changed them to be the same, saved the file, reopened it in IB, and now the 
three checkboxes are the same color.

If you don't have BBEdit I assume you can do the same with TextWrangler.

--Andy

On Feb 4, 2013, at 8:55 AM, Boyd Collier <bcolli...@cox.net> wrote:

> Glad to.  Here's a screen shot.  The problem button is Permute Genes.  
> 
> <Spagedi Controls.jpg>
> 
> and here's the nib file:
> 
> <GroupsTabView.nib>
> 
> 
> Boyd
> 
> 
> 
> On Feb 3, 2013, at 4:22 PM, Andy Lee wrote:
> 
>> Can you post a screen shot and/or the nib file?
>> 
>> --Andy
>> 
>> On Feb 3, 2013, at 3:47 PM, Boyd Collier <bcolli...@cox.net> wrote:
>> 
>>> Hi All,
>>> 
>>> I have a nib with a Matrix of one column and 3 rows; in this there are 3 
>>> buttons cells of type Switch and Style Check.  All are enabled.  Recently I 
>>> noticed that the square of the middle button is slightly darker that the 
>>> other 2.  Using Interface Builder's inspectors, I've tried everything I can 
>>> think of to see what might be different about this one button that makes it 
>>> slightly different in appearance from the others.  There is another Matrix 
>>> in the same dialog, also with 3 switch buttons, but all these are identical 
>>> (except for their titles and tags, of course).  I'm fresh out of ideas of 
>>> what to look for that might be causing this one button to look different 
>>> from the others; any suggestions regarding what might be causing this 
>>> behavior would be much appreciated.
>>> 
>>> I'm using Xcode 4.4, BTW.
>>> 
>>> Thanks,
>>> Boyd
>> 
>> 
> 

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