I have a dotted pattern I got from Deviantart. http://iosonor.deviantart.com/art/Inkscape-patterns-244793623
(second row from the top, 5th pattern in from the left side)

I did the following:
Followed the directions and selected of the object in the above mentioned squares and created a pattern with it.
Created a rectangle and filled it with the pattern.
Changed the opacity of the pattern to around 60%.
Created another rectangular (solid black fill) and moved the pattern over the rectangle using the align tools.

But after saving it as a .svg and viewing it, the opacity of the pattern is not preserved.
I tried combining the two objects but it still doesn't preserve the opacity.
I even tried saving it as a .png but the pattern completely disappears.

I'm on Ubuntu Natty, Inkscape 0.48

Welcome to InkscapeForum!

Oh yes, great patterns from RM.! I downloaded and tested, and haven't found any problems. Although in my test, I didn't change the opacity of the pattern -- only the color.

The problem with the PNG may have been using Save As Cairo png, instead of File menu > Export Bitmap, which is the proper way to preserve transparency in a PNG.

Other than that, I don't see anything that you're doing wrong. I wonder when you changed the opacity of the pattern, if you accidentally changed the opacity of the rectangle. Try starting from the beginning, but before you do Object to Pattern, change the opacity, then continue along.

Let us know how it goes

PS - I notice that you posted in SVG/XML forum, which I'm guessing is a mistake. You're not trying to do this using the XML code, are you? You're just working on the canvas, right? I'll move the topic to the Help forum