Johnny, you're stressing a lot over a $20 kit and a 500 Ms/s logic analyzer. 250 MHz would be the Nyquist frequency. If this was a normal scope channel then you would have two points for for your sin(x)/x. 1/5 of that is equivalent to 100 MHz which is a good upper limit for signals that you might use with this. There may be a bandwidth spec somewhere. I'm not sure what it is. I can tell you that even the MSO5000 with twice the sample rate doesn't do well with logic signals of that frequency. And with your clocks not being synchronized, is that enough to result in what you're seeing not jittering around? I'm not an expert on how logic analyzers are designed. Maybe I'm wrong about why but it fits what I've seen. 25 MHz seems to be a good limit based on my testing. If you want the ground planes then you should also hunt down some nice 120 ohm coax to go with it which isn't easy or cheap. Also, these accusations aren't cool bro. I didn't say that it's 4 layers or lie about anything on eBay. I stumbled across this just like you and decided to sell the extra parts I had. I have to supply you with $5 of little probe clips, hand assembled boards (placing those passives hurts my back) baked in a modified toaster oven in my kitchen, cleaning in an ultrasonic cleaner, 3D printed parts that I blow hot air on to clean up wisps, sandpaper, ribbon cable, packaging, having a car, rent, and dealing with all the other stuff like responding to people (while I'm playing the new Final Fantasy video game) and testing things. I'm sure that's why the creator isn't selling them anymore. It's not worth the hassle. But I kind of like it. Someone from Japan ordered one yesterday which is cool. And I've sent one to Australia. So far, no complaints and I think that's 6 sold so far.
edit: I have been thinking about this. There isn't a lot said in the specification about the limitations of the logic analyzer. I was bothered by the fact that the signal jitters around a bit at higher frequency but I think it makes sense. If you have a 50 MHz signal, that's a 20 ns period. For a square wave at 50% duty cycle, half of that time will be high or low. One of those state will be around for 10 ns. With a 500 Ms/s sample rate we get a sample every 2ns. So, during this short 10ns window you would have only 5 samples. If things aren't perfectly aligned you would sometimes see quite a bit of jittering around.