The ETA needs to reflect your current speed. It's expected that it goes up sometimes, since it needs to reflect the longer time if you slow down. The issue is that when you're 55 minutes away from something at 150 knots, changing your speed by 0.1 knots changes your arrival time by 3 seconds, so it takes very small speed changes to see an effect here. In fact, at 150 knots you have to be within 30NM for a 0.1 knot speed change to be less than 1 second.
Unfortunately, there isn't a magic filter I know of that can fix this. We can average your speed over a period of time, but with winds, gusts, updrafts, downdrafts, altitude changes, temperature changes, heading changes, power changes, etc, your average ground speed will still not be a constant, and the system will still count "backwards" sometimes, and will still seem stopped sometimes as the filter adjusts to the new condition. At some point it needs to adjust for the fact that your speed is different that the current displayed time. Given the original use case of the seconds display, we also can't filter for very long because all filters are inherently delays. Put in a big filter, and it will show no change in ETA as you change speed until much after the speed change, and then people will wonder how long after a speed change they need to wait to trust the number.
All this is to say "don't blame the filter" because there isn't one that can do much here and still make it useful. We'll put an option to hide the seconds on the request pile. It's the only way to not have the seconds digits do distracting things.