You're correct, each sphere is treated as a separate single target spell.
There's some kinda scary potential there in a best case scenario, you're paying quite a lot for an item that doesn't help you out much otherwise though so it's currently working as intended. It's something we'll keep an eye on just in case though of course.
Why was this changed? So far, all of the changes to Syndra have been good, but this one is flat out bad. By changing this, you remove the reliable method to grab your sphere. If the sphere is in the middle of minions, or if a crazy team fight is going on... I rely on this mechanic to get my sphere instead of a minion or something else. I am aware of the fact that the W prioritizes the sphere if you hover over it with a minion there, but it doesn't always work, and sometimes grabs a minion anyways. The "grab nearest orb" with the W was buggy (required a couple button presses sometimes) but it was extremely useful to ensure you'd grab your sphere.
Now, this reliable method is no longer possible, and it will grab whatever is nearby... and yes, I just tested this on the PBE. Riot, please reconsider this change. I don't believe you intended it to be a nerf, but it is. There is very little gain from this quality of life change in terms of Syndra's playability, but it also brings a nerf to those who play her very often.
Regarding having to press the button a couple of times sometimes to grab a sphere I'd love any further details anyone's got on that. I've observed it happening myself but can't repro it on demand.
The initial grab's always had a small check around the cursor for nearby units (nearest unit within a few hundred units) if something's not directly targeted. Is it possible that's what you were seeing?
Regarding the W not grabbing I've seen that occur even when the sphere and cursor are both well within the spell's cast range so there's definitely some other cause.