I'm gonna recheck the wiring and maybe bi wire it again,
You're missing the point. There is no benefit to bi-wiring, so please don't go on a useless snipe hunt doing that.
There IS a problem: your room correction software doesn't pick up the bass extension your mains are capable of. The speakers are either not producing it, hence the inquiries about having the jumpers in place, or the mic isn't picking it up (possibly due to a defective mic, or placement of the mic in a null mode when taking measurements). If it's a faulty mic, or wonky automagic software problems, you might have to bypass it and trust your ears.
Test the speakers full range, no subs. If the jumper is in place, and the speakers are fully functional, they should extend nice and deep. If they don't, you've identified the problem. If they do, continue your troubleshooting process for the next most likely culprit, which could be a measurement anomaly or even a faulty mic.
Can you adjust the crossover settings manually to override the automagic settings? If so, set the hp for the mains one octave above their f3 (with corresponding lpf and level for the sub) and give it a listen.
With your speakers so deeply corner loaded I would expect considerable reinforcement of lower frequencies, which typically tricks these automagic setup programs into setting the hpf too low, rather than too high, as in your case.
