This has been happening to me for months now intermittently, where I upload a bunch of vectors with a matching jpg, but they don't get matched properly by SS. Either it comes up with the "no corresponding jpg" error message when I go to content editor, or if that doesn't happen then the jpgs show up in the Editor but no vector.

Or another variation of the problem is it does occasionally match them correctly, but then creates duplicates of the vector.

I have tried both FTP and web uploader. Web seems a little more stable but still FAR from right.

How are you guys who deal with hundreds of vectors managing this? Or is it just happening to me....?

I happen to upload both normal JPGs and Vectors from time to time.
Like all sites SS server needs to process your uploaded file before it becomes availible to you for editing. SS's server is actually very fast, so you normally do not have to long to wait before you can access your uploads. The problem however with Vectors are that they have to be available as as pair (eps/jpg) when you access them. So if you go onsite to quickly (before all the pairs have been processed and made available) you will actually be interrupting it in its process. Depending on your upload order you might end up with only the EPS or JPG file.

To reduce this problem I found that if you wait at least 30 min - 1 hour before accessing the site after finishing your vector FTP upload, the chance of this problem occurring is vastly reduced.

Just my experience. Hope it might help you.

I seem to have this issue occasionally when working from Illustrator CS6.

If I save them from CS4 it seems to work each time.

Ah, might be the difference, as I save mine as 8 EPS as being the lowest requirement of the sites I submit to.