I found this topic:
http://electricmotorcycleforum.com/boards/index.php?topic=4857.msg32956#msg32956 but the forum warned that it had been more than 120 days since any activity and I should start a new topic.
2 weeks ago I bought a new 2017 FX with 61 miles. The front brake was squealing a bit when I test drove it but it became unbearable after I took it home and rode it just a few miles. I sanded the pads, chamfered the pads, and used the Loctite squeaky brake goop, but nothing made any difference.
I took the caliper off to inspect closely and checked the rotor closely. All the button head screws holding the rotor to the hub extended 4 mm or so past the inside of the hub and one of them was impinging on a spoke. The parts catalog said 8x20 but I bought 8x16 replacements and they just come flush with the hub. The one original impinging screw left a mark on the spoke so it was touching it if not bending or affecting in some way.
Anyway, I don't think the bolts were affecting the squealing noise - just didn't look right to me. I realized the pads are the same as the front of my 350 KTM so installed a spare set of Rocky Mountain Tusk brand pads I had. I didn't use the thin metal clip ons which may be designed to reduce squealing that were on the original pads. The noise is gone and braking is fine. As others have reported here, it seems like the pads were the problem.
Otherwise, the FX is great and the EM is a whole different and very cool experience. I still plan to make some changes later and use it for trail work and other off-road fun.