Probably a silly question, but what is the voltage on pin 2, is it 3.3 volts ?
Could it be a power issue where the LimeSDR is not getting enough power and what it thinks is 3.3 volts is a lower voltage. And because of that it is not behaving like a standard 3.3v CMOS&TTL for Vih.
Here my other “board” is an Arduino, and when I check what that Arduino outputs, it’s sometimes quite low, around 2.7V. When it’s like this, the Lime doesn’t see the GPIO as HIGH.
I’ll check the voltage on pin 2 when I’m back at my computer.