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I think the problem is being caused by a buffer that is connected to the lines.
There is a std 74lvth244 buffer that both signals are connected to. I think
the bus hold circuitry is latching the inputs low on power on. I am going to replace the buffers with a non-bus hold type and see if it fixes my problem.
Phil
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I have verified that our config problem was caused by a buffer with bus hold circuitry.
We disconnected the buffer and the config lines were pulled up normally. We will switch to a buffer without bus hold circuitry.