Hi,
I do this all the time, and my results are pretty much spot on. I use the stitched images in image analysis procedures, so any changes in colours would have an enormous effect. What I find though is that you need to make sure all the images are captured
with the same white balance and exposure settings, and that you need to perform a shading correction. The last can easily be done in ImageJ or similar software. I've customised the standard shading correction plugin for imagej by only correcting the brightness.
if you want I can get you the modified plugin. However, the standard one works pretty well in most cases.