Sorry for the confusion. The Custom Colors feature will update the color values if the color you set is too close to the background color and may affect readability or make it harder for the sight-impaired to read it.
You can still override the colors, but you'll have to do it with the CSS Editor instead of Custom Colors. It may take some work if you want to change a lot of things, but the forums are a good place to ask for help.
I checked your site, and I found that it looks like you've already got the link color updated using the following custom CSS:
a {
color: #ff542d;
text-decoration:none;
}
#topmenu li a:hover,
#topmenu li.active a {
text-decoration: none;
color: #ff542d;
}
.post .title a {
color: #ff542d;
padding-bottom: 5px;
}
To also update the flickr link color, add ".widget ul li a" to the selector list. Note that you can combine those. For example, you can replace the first two blocks from the example above:
a {
color: #ff542d;
text-decoration:none;
}
#topmenu li a:hover,
#topmenu li.active a {
text-decoration: none;
color: #ff542d;
}
with this:
a,
#topmenu li a:hover,
#topmenu li.active a,
.widget ul li a {
color: #ff542d;
text-decoration:none;
}
Notice that I added ".widget ul li a" to the list in the last example.