Do the fibre converters offer any diagnostic capabilities? A slightly dirty fibre ferrule or damaged fibre might be causing drop-outs. If the problem is only marginal it might affect throughput without being immediately obvious.
What about jumbo-packet support? If they don't support jumbo packets but your computer and server expect it, you could easily see a halving in performance, if not more.
Edit: Cleaning fibre ferrules must be done with care. It is very easy to scratch the most critical parts of the fibre at the centre of the ferrule (which are only microns across, much thinner than the thickness of your hair).
When I was working on a fibre polishing machine, I would test the quality control systems by deliberately dirtying and then cleaning them. Dirtying them was easy, just some finger grease was enough for our QC system to measure significant back-scatter losses.
When it came to cleaning them, I would take a small, fresh piece of lint free cloth and wet half of it wih IPA (Isopropyl alcohol). I would then swipe the ferrule once along the we side of the cloth and then once on the dry. This was generally enough to get a perfect signal, unless the ferrule was damaged - in which case it has to go back into the machine to be polished again.
One thing that you should not do is use the same piece of cloth more than once (it is very easy for the ferrule to pick up dirt deposited on the cloth by a previous swipe), scrub the ferrule over the surface (as previous comment, but also more likely to scratch the surface) or apply too much pressure (you don't want any grit in the cloth to gouge a scratch in the ferrule).