HTML ImageShow will overwrite files called the same, inside the same named folders "big" or "thumbs". So, most probably you overwrite HIS's own output... I don't think you really lost such an amount of time, sorry.
HIS *will* create "image galleries with slideshow capabilities". Have you tried the "start slideshow" button, BTW? Just google for "the image slideshow" (including quotes) and browse some image galleries with slideshow capabilities.
In fact, I use HIS myself because it's free and I like its features better than other freewares. Output may be ugly and may be fixed in a future, including templates and a bunch of features (this will be in a future). But just don't say, please, it doesn't create slideshows ;-)