The problem with the juggernaut was definitely mitigation/gear -mainly mitigation- he sounds like an immortal specced jugg w/ good pvp gear, you shouldnt be doing a lot of damage to him, classes that do are only able to do so because of some serious issues with mitigation atm
see this thread http://www.swtor.com/community/showthread.php?t=155034 for a better explanation on that.
as for the marauder i dont know, as you are engineering and your not saying what your engineering abilities, you are just mentioning basic abilities like snipe or SoS. which are definitely not engineerings main source of damage.
Spec aside marauders are a tough fight for us, our main advantage being range, just remember leg shot is your friend, and watch their buffs for their defensive cooldowns, so you dont waste precious energy on someone who will shrug it off for the next 6 seconds.