if you dont have a sitemap yet then add one. also, keep working on getting more backlinks which will let search engine bots make frequent visit so that all of your pages get indexed
This is something that happens with newer sites you should create a sitemap if you haven't done so already and start building backlinks to your sub-pages.
We had the same problem once when we used Macromedia software to create submenus - Google couldn't follow the links and so stopped indexing our pages. We changed to a different submenu system and every page is now reindexed and the site is no 1 on Google for most of its target keyword searches.
fluctuations are normal, the number of pages indexed will decrease and increase from day to day, just as the tide comes in and out. however, if your number of pages indexed steadily decreases and stays at a low level with barely any fluctuations, you have probably been sandboxed or hit with some kind of penalty.