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and for some reason it cropped the image.
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Perhaps one image did not register properly? After you do the alignment, blink all the images and watch the alignment numbers for each image. Look out for ones that seem excessive or report an error. You will need to remove these before you do the stack (select the image and press control-R)
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what is the tip to get the colour channels aligned?
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No trick really, just align all images in one shot to the same image (best to use one from the L filter as the 'base image') and don't forget to check for errors as mentioned above then click 'apply'.
I used the CCDIS plugin which works a treat.
Then stack all the L, R, G and B into 4 separate files. Then select color combine - it should work.
Still stuck? The program help is really good a worth the time to read.
James