OK, so it's a shifter cable/hub gear alignment issue.

When your shifter is in the middle (2nd) gear, the end of the indicator chain needs to be 1mm out from the end of the axle for all the gears to engage smoothly. All the hub gears are switched from this baseline point. If this point is off alignment, you'll get intermittent engagement of all the gears, not just the middle gear.

You adjust the cable slack by means of the (long/top) barrel adjuster to get to that 1mm out position. Once you get to the 1mm out position, you use the shift cable (short/bottom) barrel adjuster lock to keep it in that place.

Typically what happens with new shift cables is that they develop a little slack as they wear in. That's why you have the barrel adjuster, to take up a little of that slack and get everything back to normal again.