If you change a node's time outside of kOS, that change is not visible in your script.
print (nextNode:time - time:seconds) + " " + nextNode:eta.
3636.70990401506 3636.70990401506
// manually drag node along orbit, then
print (nextNode:time - time:seconds) + " " + nextNode:eta.
3626.90991336107 6676.74107664824
If you read another suffix first, the time suffix starts returning the correct value.