I have the low e string problem too. Most noticeable on Lester pickups. Not there on some others. JTV-59. To figure whether it is a firmware problem, I reverted to Flash 1.9. The effect was much less, barely there. Couldn't check it out very much - 1.9 doesn't support interface with the HD workbench, so mixing and matching is very difficult. But reverting from 2.23 to 1.9 definitely made the sound of the low e string much closer to the others on the Lester pickups. I loaded 2.0, problem was back. I have gone back to the latest, 2.23. The 89 Neck seems to be better than the others. But I wish the E string didn't do that. As a note, when I bought the guitar used, the low e string had the crud problem, about half the output of the other strings. Cleaned the bridge, level now same as the rest. But way twangier than the rest when using the humbucker simulation.