I have had this problem on 80m since new, trying to run fldigi. Have not tried ft8 as I recall, and I don't think I have the problem on other bands but I only work 80. Dummy load tied to my HF-AUTO also has the problem. I too have talked to the factory, but it was a number of months ago. They had no answers at that time other than they think it is an antenna / feedline issue. Given my problems with the dummy load, I have my doubts. have you tried skipping the tuner and running direct? I also tried that and it did not help, my native SWR was 1.6:1, tuner made it 1.08:1, amp reports 1.3:1 until it kicks out.
Unfortunately my antenna was just taken out last night by a big tree, but when I get it fixed I will try more testing. What version of software are you running in the two units? I am running the latest according to the web site.
Al? KD2PNR