Cyclone IV E JTAG issues - VCCA voltage level

Well,

that sounds very strange.. if there is nothing on the "Output side" of the tiny logic that has a low impedance (or is a high capacitive load) that kills the TDO Output when driven by the cyclone, I'd assume there is still something strange on your board... Nevermind the Input of the tiny logic is a very high impedance thus I'd still assume either the supply of the TDO "bank" is not as stable as it should be or the board has some bug on the TDO line.

Have you checked the TDO Signal on the tiny logic Input to be a valid Signal? Otherwise - I'm afraid - this fix might not last very Long...

But that should not minimize my lob for your work on the Problem :-D