Are your slideshows at the top of the page? Read this tweet (from the czar himself) which says there was a refresh Feb. 6th of the page layout algorithm. Cutts: https://twitter.com/mattcutts/status/432940645200588800
It targets ads above the fold, but seems to indicate that lack of written content within easy viewing reach can also be undesirable.
Read more about the algorithm here: http://insidesearch.blogspot.com/2012/01/page-layout-algorithm-improvement.html
Other possibilities may be that the text in your slideshows isn't html, or you don't have alt tags for the images, or the slideshow slows down the site, or that's all you really have for content on the site? Some slideshows are just not SEO-friendly, aside from algorithms and the case that they are generally not user-directed, and hence not user-friendly.
Good luck! Sounds like the the kind of haystack I find myself rummaging through as we speak;)