In general hamstring soreness or soreness behind the knee results from a saddle that's too high or too far back on the rails. It's a bit unusual to have soreness high in the hamstrings as it's more common to feel stretched or sore in the lower hams right above or behind the knee joint.
Rather than randomly moving the saddle down, forward or back you can either set your bike up on a trainer and capture your working angles at the top and bottom of the stroke. Good info on what you'd expect for angles here: http://bikedynamics.co.uk/guidelines.htm
Or the other quick sanity check is to see how your total saddle height compares to your greater tronchanteric height.
Basically find your greater trochanter as described here: http://www.google.com/imgres?um=1&hl=en&client=firefox-a&rls=org.mozilla:en-USfficial&biw=1259&bih=583&tbm=isch&tbnid=-t9MC_SWkTvSeM:&imgrefurl=http://pinnaclept.wordpress.com/2010/04/05/self-muscle-massage-pt-5-lateral-hip/&docid=RT9CIceXZamkIM&imgurl=http://pinnaclept.files.wordpress.com/2010/04/greatertroch.jpg%253Fw%253D600&w=400&h=394&ei=jOAeUJjQHKWViQKG1YCICw&zoom=1&iact=hc&vpx=593&vpy=129&dur=440&hovh=223&hovw=226&tx=88&ty=110&sig=105147305253098613675&page=1&tbnh=122&tbnw=124&start=0&ndsp=23&ved=1t:429,r:4,s:0,i:85
Measure the distance from the floor to your GT while wearing your cycling shoes (yeah, weird but that's how the original studies were done), you can mark a spot on the wall or have someone else make the measurement but stand upright with your feet about as far apart as your pedals.
Your total saddle height measured from the center of the pedal spindle to the top of the saddle (where you actually sit on it if you sit far forward or backwards or use something like an Adamo saddle) should be in the range of 96% to 100% of your GT height. The higher end of that range corresponds to max knee angles in the 145 to 150 degree range as shown on the bike dynamics site. It's a fairly wide range of acceptable seat heights for best power/O2 utilization but you don't want to have your saddle higher than 100% of your GT height as power and efficiency tends to drop rapidly when you go too high not to mention hip rocking, chafing and other issues.
But yeah, as a first guess I'd suspect your saddle is too high or pushed too far back but wouldn't jump to change things until I had a good view of your overall fit including cleat placement.
And of course a good fitter should be able to sort this out pretty quickly or at least let you know if it's not a fitting issue.