Here's a typical example of this problem, the picture get's darker toward the upper left, and there is a large dull spot around the upper large palp of this beetle larva's head. The dark patch is due to dust on the CCD of my webcam, it casts a shadow on the sensor. I know this is not a very good picture but it illustrates the principle.
Below is a more balanced picture.
To acomplish this transformation you need a picture of nothing, or rather a picture with the imperfections only.
Then you use this to adjust the brightness of the first picture to get the second.
Load all of the frames to be stacked into CombineZ, then load the correction frame. Note you must correct the original frames not the stacked image, this is because sizing and aligning the frames will alter the position and size of the imperfections.
Now with the correction frame visible click on 'Make Active Frame 2' which is on the frame menu.
Press the down arrow once to show the first frame to be corrected.
Next click on 'Correct Brightness' which is on the '2 Frame Functions' submenu on the Rectangle menu, this will correct your first frame.
Press the down arrow once, to reveal the next frame to correct.
Press the Return key, and a dialog will appear accept the default i.e. press return again, the second frame will be corrected.
Repeat the last two steps (down, return, return) until the whole stack has been corrected.
Now stack as normal.
There are refinements possible to the above basic procedure.
First to get a better correction frame take several pictures of nothing and average them together. To do this start CZ from fresh, load the pictures of nothing, click on 'Sum of Stack' which is on the 'Input' sub menu of the filter menu, now press 'A' once to select a rectangle the same size as the input pictures then use 'Save Rectangle As' which is on the file menu to save the improved correction frame.
If your camera exaggerates the amount of imperfection in the picture of nothing you will need to alter the amount of correction applied. After 'Correct Brightness' and before moving on to the second frame to correct you can alter the effect. to do this press 'M' and 'N' to alter it in large steps and the Left and Right Arreow keys to do it in small steps. The changes will not be saved to the frame until you press return.