Take a picture and post it. If it right where the deck meets the gunwale my guess is that either the radius of the inner liner failed and CRACKED due to unknown stresses or someone else did a S#!++y job replacing the floor at some point. Either way your going to have to grind away and re-glass. Caulk or adhesive ain't gonna cut it...You might start by doing a search of deck or floor replacements and read Strick's post "Here we go again" at the top of this forum. If you explore this very forum to your heart's content, you'll probably gather enough knowledge to add a DSR (Doctorate of SeaCraft Restoration)to your resume'
Good luck.