This isn't in anticipation. I'm wondering if the newer models are having problems. Mag's are the only difference, but the quality of manufacturing can change as builders become experienced. Also the Standard's bridge is different from the 69's. I just haven't seen any mention of 59p, 69s, or the standards. If it's affecting standards then it very well could be a software issue. But I haven't seen anyone mention them. But if it was software I would think downgrading and applying the latests firmware would eventually solve the problem. It would finally install correctly. So that would leave electrical or physical/mechanical. I'll try going through more pages, but there iss a lot to read. Have people tried changing bridges and therefor pickups? At almost $200 I would imagine most haven't. That also could be the reason L6 hasn't come up with a solution. They would rather you eq (free to them) it out than replace a bunch of expensive parts.
I've worked for manufacturing companies. The guys you are dealing with more than likely want to help you, want you to be happy. It's the people at the very top of the totem pole that stop them. They get so consumed with profit margins that they forget that making customers happy is important.
This problem bothers me. Not because it's affect me, but because I'm a problem solver. It's what I do. 2 1/2 years is way too long. In fact it shouldn't have taken more than 6 months to know and understand the cause. Of course if you're in denial of a problem you can't even start to fix it.