Page Links to items & categories Disappeared but categories Qty Still Show

[lonestar]

As I usually do frequently, I visited my web site, lsbags.com , and was greeted with a warning strip across the top of home page, which read ! Warning! User Permissions Changed-This may be a Security Risk; with /home/adminman/public-html/cart/includes/configure.php Url... :'( Other than having some problems recently with email, no problems with the main functions,html,etc have been apparent and no changes to any functions had been made. Although I reset the permissions to eliminate this warning, I then noticed that links from categorys to items are missing. The shipping, conditions ,etc links all are working,(and the few scattered links on home page, specials,new) but the individual products are not. Please visit the site at www.lonestarbags.com (lsbags.com) and see for yourself my problem. Click on the categories and nothing shows!(although item qty clearly is there!) Could this be a server issue with my host? Any and all help would be greatly appreciated. :D