MultiUpload does not work since the upgrade to the latest MediaWiki version..
This is a known issue and as MultiUpload is effectively abandonware, we'll likely be forced to retire it for the time being until someone can patch it, I'm afraid.
(For what it's worth: I've spent quite a few hours looking into this and it seems to be non-trivial to get MultiUpload working again. I'm not even sure *what* the breaking changes between 1.32 and 1.34 are and what classes are affected.)
I think Rose-Biblio is one of the largest wikis in shoutwiki and you must earn some money with it by advertisement on my sites. Spending "a few hours" could be a little bit more! Working with singleupload is not acceptable for my needs.
It brings in some ad revenue. This year to date, about enough to pay an average UK web developer for about an hour and a half. However, as one of the largest wikis, it is also one of the largest contributors to cost. ShoutWiki doesn't have paid staff, not for ideological reasons, but, for financial.
MultiUpload isn't the solution to the problem, whatever way you look at it. We're not discounting a feature to upload multiple files being implemented in the future - there's an alternative solution to review already on my todo list (the one that includes fixing the outstanding list of other 1.34 related issues, HTTPS, answering the lovely backlog of support tickets, unfortunately, all more pressing than this), however, as Jack stated, the MultiUpload extension requires very extensive rewriting to have it work in a similar way, that isn't "a few hours" of work.
My honest suggestion, for the time being, would be to look at uploading them via the API either by directly scripting something or using a tool such as Pywikibot (other options are probably available, I'm not familiar with everything that exists)