First of all, does it even matter? Are you dissatisfied with something about these beers that makes you want to change your brewing process? If the answer is no then who cares what the software says. Or, for that matter, what the FG is.
Healthy yeast are definitely driving better attenuation but you don't want to get away from healthy fermentation. Look at raising mash temperature and/or shortening your mash to keep more dextrins for body.
It does matter more to me when brewing lower gravity beers. Not as big a deal to be .5 to .8% abv off with a 7 or 8 percenter, but its a much bigger deal to be off like that on a 3.1% mild or bitter. Those types can be light enough that that much additional alcohol can throw off the balance of the beer.
has the beer tasted unbalanced? again, the point is that what matters is the perception of the beer and conformance to any particular set of theoretical numbers doesn't necessarily equal any particular flavor profile.
so if the problem is that the beer tastes a little off balance due to alcohol then I would say you should attempt to change the fermentability of the wort or choose a less attenuative yeast or a yeast that leaves a better mouthfeel to balance the impression.
Crystal malt is good for this as is flaked barley, rye, or similar semi-raw glucan rich adjuncts.
You can also play around with yeast handling. I would say that pure o2 is not appropriate for low OG ales. try aerating by hand with a whisk or mix stir. try keeping the ferm temp even lower and/or raising the mash temp to 162.