Dear Karl
Thanks for the reply to my questions. You have certainly explained what you do.
When I mentioned linearity I didn't mean colour linearity but linearity to increasing exposure time. This applies to CCD cameras but I don't really know how to apply it to your camera. What is the range of exposure times you can do?
Is 2.56sec the maximum?
If so you need to to a test.
Find a brightish non variable star that is near to the zenith. It needs to be bright enough to register with a 0.5 sec exposure.
Take 5 frames at 0.5, 1.0, 1.5, 2.0, 2.5 sec and dark subtract them all. Don't do any stretches or other processing.
Measure the magnitude of the star in each frame using a single star tool using an annulus that includes most of the star image. (that I hope maxim has. I don't use maxim so I'm not sure of the name).
It should give you a total fux for the star and maybe a max pixel level and a magnitude conversion.
Import the data into a spreadsheet.
Average the results for each exposure time.
Work out the flux/sec if maxim didn't give you the magnitude conversion.
If the camera has a linear response then the results should be the same in each exposure.
If the camera has some sort of antiblooming, it will not be linear above about 1/2 the saturation level.
Once you know the level that you camera has a linear response to you can know what data in the single frames you can use.
You can stack images for photometry but only "average" and "sum" are valid. These will increase your signal to noise but nothing else.
The catalogues you mention are all very crude for photometry and can't be relied on at all for measurement.
You are better using the values from the AAVSO by producing a chart here.
http://www.aavso.org/observing/charts/vsp/
An easy star to try to begin with is T Aps deep in the south. It is currently about mag 11.5 in V.
You need to use the comparison values from the chart not from the other catalogues. The technique is called differential photometry. Measuring the magnitude of a known star and your variable star in the same image.
You then can work out the correct magnitude of the variable star from the measurement you took of the known star.
Hopefully this will help.