wierd temp problem

Hi all, I am having a strange problem with my Ecksbot printer that I built in 2012. I have fixed/repaired almost everything on this printer through the years, but now have a problem that has me stumped. I had a thermal runaway that burnt up my hotend. I replaced the hot end and thermistor and thought I was done, but in repetier if I start a print, the temp doesn't change as the bed or hot end are heating up. If I let it go, it would just burn up the hot end again. I have changed out the ramps 1.4 board, reinstalled the repetier software, replaced the thermistors and don't know where to go next. When I connect to the printer, it shows room temp for both the bed and hot end. If I activate the bed or hot end, the shown temp values stay at room temp even though they are getting hot. If I stop everything and disconnect then reconnect the printer it shows the temp that they warmed up to before I shut it down, and then stay at that value. The fact that it reads the temp when first connected rules out the thermistors. I am missing something. I am using a mega2560 with ramps 1.4 with Marlin firmware and repetier host to control it. Any idea's?