A WebmasterWorld thread notes that if you do a site command search using SITE: versus using site:, Google will return different results.
For example, lets compare site command results for the Search Engine Roundtable.
- site:www.seroundtable.com returns about 7,990 results. - SITE:www.seroundtable.com returns about 148 results.
In the lowecase version, you see:

In the uppercase version, you see:

Notice how Google is finding results for the phrase "SITE:www.seroundtable.com" in our uppercase version. In contrast, in our lowercase version, Google is returning the number of pages they found indexed.
Why is there a difference? I am not sure.
Forum discussion at WebmasterWorld.

Comments:
gabs
06/08/2007 12:05 pm
Same for all google commands http://www.google.com/search?hl=en&q=LINK%3Awww.seroundtable.com
Amit Verma
06/08/2007 12:53 pm
But I am not getting any results with capital commands.
TOMHTML
06/08/2007 12:54 pm
Just because it's the same search as [site + "www.seroundtable.com"] ...