Registax is driving me absolutely nuts!  I have followed a few different tutorials and am finding the aligning step to be the killer.  I am using 9 or so TIFF frames of the moon shot with a digital camera. . .no scope. . .and the images are pretty well defined.  Now if I have understood correctly, I choose one frame and select my alignment size box size and apply it to one frame.  Then, hit the alignment button.  This is where the wheels come off the wagon.  Only one or two frames align.  Even when I put my quality selector at a lower rate. I have tried all manner of attempts and have always ended up this way.  Anyone that has had a similar problem and found a way to correct it, please help.  Thank you on advance. . .I'm losing my mind with this program. 

What are you trying to align?  Are you using a single or multiple alignment points?

Planets usually use single big one, the moon usually requires several small alignment boxes. 

CFB

 Oh, I'm processing moon shots. I've tried both the large alignment box and several small ones.  When I use the small ones, my image turns out fragmented and incomplete when I stack them

When you use multipoint alignment, try to find features that are in every image and has high contrast.  For example, a very clear peak or a bright reflection near the terminator.  Be sure that all the features selected are in the box.  It sounds like the alignment features you are selecting are not constant in the images.

CFB

 If you're taking your photos with a fixed tripod or other type mount that isn't actually tracking the moon and using a regular digital camera, each of your images is in a different spot in the frame. It's probably too much displacement for Registax to handle.

 Thanks jonm, that made the image align a little better.  I still need a bit of work on getting the image tighter but you were definitely right. thanks for the help man.

 Well, I've been trying to "manually" align the images on registax.  Am I correct in assuming that it means that I can place the images where they need to be rather than have the program do it?  Any tips on this?  I have been playing around with this thing all day and have not made any progress. 

put your camera in video mode, like take a movie of the moon drifting from one side of your lense to the other

30 seconds or so

 then , get a program called bink and smack  off the internet for free to convert the video files to AVI, if your camera dosent spit that format already.

use the multi-point on the lowest setting,( 32 or something) and let regi-stax determine which is best ( auto)

set your quality to around 70 or 80% to weed out the air flux

optimize,  and stack

heres an example of what my crap point and shoot can do ($150.00 camera pointed at my 25mm eyepiece , or afocal method) with this method