OK. That's what I use, so I know it can handle 3 AIUs, at least without any accessory relays being locked on. I wouldn't expect the resets to cure the problem, and doubt that the software would be the issue; I use 5.0. Are you sure that the cable you string from AIU#2 to AIU#3 is good? Try putting it between TIU & #1 or between #1 & #2 to test if that makes a difference. If the wrong port on the TIU has ever been used, that could damage an AIU.
I have no ready answer to your second question. Is it the same cable you use for the other TIU? If not, try the other cable. USB cables seem to fail more often than other types (at least that's my experience. Since only 1 of my 4 TIUs is a Rev L, I use a serial cable for all upgrades, which I do all at one time.
There may be a delay in other gurus responding. They're mostly all here at York,