Hello Alfed,
I have a costum PCB with a EP3SL50F780 on it. Till now I had no problems with JTAG-configuration but I had this temperatur issue that u are describing... In fact, the FPGA temperature goes up till 50°C with a simple 'counterdesign' and till 70+°C with our complete Design. What temps do u have?
Yesterday, the JTAG-config stopped working. I thought it's because of the temperature issue but now I'm not so sure anymore...
Are u sure that ur I/Os are sinking/sourcing instead being HighZ? This would be wired but if u are sure it is the reason why your FPGA is getting hot.
regards,
helac