One thing to consider...
"Nether Grasp's suppression can be removed by
Quicksilver Sash, 
Alistar's Unbreakable Will, 
Gangplank's Remove Scurvy and 
Olaf's Ragnarok," as well as if you are interrupted since it is a channeled suppression.
http://leagueoflegends.wikia.com/wiki/Malzahar/Strategy
I'm well aware of these, it is definitely not that. It is an interruption and not a prevention or removal of the suppress.
If unrelated...
Which map do you notice this on? Or N/A?
Mainly summoners rift, I do not recall having these problems on twisted treeline, but I am not sure.
It almost sounds to me like the enemy, such as alistar or poppy, charge at you right before you ult, and they finish their spells interrupting your sustain. Is this the case, or no?
Nah, I've had that happen a couple of times when they've charged or whatever right before or as I ult and it's gone through, but that's noticeable.
Because, and someone correct me if I'm wrong, I don't think his sustain cancels spells. I'm not completely sure about that though.
Maybe there are cast times for everything and we both use the skills at the same time? Not sure, might have to check while playing against someone I know to see if we can test it.
I've been stunned by Syndra (complete q-e combo) while my ult was active on her without her having QSS so yeah, quite confusing. It's like anyone can just wait to have a stun and press it just as they see Malz ult.
In a recent game in a 1v1 against a friend to test some of these, he was Rammus and he was ulting and powerballing towards me. I ulted before he got to me and we both agreed Rammus continued for a moment while the nether grasp animation was active and after taking one tick of damage then he stopped, resulting in him getting his ult into range.
Similar things happened with his taunt going off just after the beginning of combat between us. Neither Rammus's taunt nor nether grasp are known to have a cast time or delay, so if both are used at the same time only one will activate first and so only one should go on cooldown right? I accept that sometimes abilities are used so closely together that you never see the animation for it (like if I never saw nether grasp actually activate, but it still goes on cooldown, which happens sometimes, though shouldn't that only happen with interrupts that take time such as sion's stun's travel time?), what I am reporting here is his ult animation becomes active, and even does the initial tick of damage, but then is interrupted.
