I am also having the same issue when attempting to use multiple slideshows within different section of the site.
Despite creating another version of the module, changing settings such as image height etc and publishing on different pages ALL instances of the slideshow demonstrate the SAME configuration settings which is annoying.
My site is still local so can’t be checked BUT this must be an issue with the template.
Could JA check the demo site and test publishing a copy of the module in another section with different configuration settings to resolve the issue.
Hopefully it can be solved.
Thanks
EDIT:
Just found answer here:
http://www.joomlart.com/forums/topic/ja-slideshow-image-update/
Change profile settings – I made a clone then changed the one slideshow parameter I required which was height of images then saved. My 2 examples of the JA Slideshow are now using 2 different ‘profiles’