When signals don’t look as I expect I often turn on analog capture for the problematic inputs. Often the trouble is the input voltage is near the digital detection threshold for the input, or edges are slow or noisy. Even if you can’t see fast edges or pulses in the analog capture it can often help just to see what the voltage levels are.
Note that the analyzer currently filters the analog data so it is hard to determine where the actual samples are and when the sample rate is low compared to the sampled data the smoothing provided by the filter can be very confusing. Saleae are going to fix this, aren’t you Saleae?