I wrote what is root cause in my case 
And your test was little too simple with Ubuntu. Did you check if XHC1 is enabled or disabled? Also appropriate PCI bus power where USB is connected. Also is there any script in Ubuntu which is run on suspend/resume to disable USB. I tested Ubuntu too and resume from USB didn't work. Which means it was disabled somehow. And because of that it is useless to me.
And even disabling USB in my case suspend/resume is hit and miss - it doesn't work 100%. Don't know why.
Btw: my system is SolidPC from Solidrun if that matters. And I talk about this issue with one of their specialist (who told ACPI wakeup tables are wrong - probably). They didn't investigate issue I assume because didn't get any more feedback.