G'Day Starcrazzy,
You might need to describe a little more fully what you are doing in order for someone to say what's wrong, but I'm happy to tell you what I do. Hopefully, you will find something that you aren't doing or do differently... and if I'm really really lucky, someone will tell us both that there's a better way!
I have taken my darks both as a few frames on the end of my capture avi, and as completely separate avi's (also as single frames on my C5060WZ). Either way, I stack the dark frames in Registax and save them as a BMP file.
Then I select the avi/images I'm going to process, and the click on the "Flat/Dark" button at the top left of the registax screen. Chose "Load Darkframe" and pick the darkframe BMP file that I've just made.
Now before you hit the "Align" button, make sure the "Darkframe" checkbox in the "Use" controls box is checked.
Everything should work...
Now, I should mention that I have been having some problems with my darkframes... If I stack images without a darkframe, everything's cool... if I use a darkframe the dark background of the image goes psychadelic colours. If that happens to you, it is something repeatable and we must be doing something wrong!
Hope this helps anyway!
Al.