My guess is that you are not finding any such boundary irregularities because Congress tends to establish non-natural boundaries as high-level latitude and longitude definitions without regard to the existing PLSS boundaries. The Kansas-Nebraska Act, for example, fixed Kansas's southern border at the 37th parallel north. Thus, if there had been any jogs in a pre-existing PLSS boundary on this parallel, they would have simply been ignored in favor of following the boundary as defined by Congress. If there was not adequate surveying to establish where the desired boundary ran, Congress would likely have provided it as a matter of regulating interstate commerce.
Meanwhile, at the state level, it is much more desirable to follow existing PLSS section lines in setting county boundaries. Doing so means the state can use the existing, already drawn lines rather than have to pay to have new lines surveyed and monumented. It also means that county lines are less likely to bisect existing municipalities or properties (or if they do, they at least do so in a way easily describable through legal language and thus more easily understood by the legal system). In more modern times, section line roads exist, meaning that the line itself is for all practical purposes tied to a physical object easily understood by laypeople.
State and county governments also have a lot more at stake because they are more likely to have to deal with a constituent angry about an inconvenient political boundary negatively affecting them on a personal level. Congress, however, is much less likely to feel the need to be responsive about such trivial matters. (Congress also had the pleasure of drawing most of their boundaries before the areas they were drawing them through were settled by Europeans, so there was less of an incentive to follow pre-existing survey lines to begin with.)
