No, it's clearly a software issue, I don't think it would make sense to ask for a replacement which would most likely have the same problem (assuming that they accept to replace the phone). If it's a firmware bug, it will sooner or later be fixed. If you had this problem even before rooting, it might be related to some app we have both installed. In case you find out more, please let me know, I am also going crazy for this little annoying issue!
By the way, after my last post, the volume buttons kept working without problems until I next rebooted the phone, which was several days later. Now they are again not working. -.-
Current phone: HTC One (M8)
HTC HD2 (Dec 2010 - Apr 2014; thank you Leo!)
HTC Touch HD (Dec 2008 - Dec 2010)
HTC Touch Cruise (May 2008 - Sep 2008 [stolen])
Previously: Nokia 6630, Nokia 3510