Im glad to hear they haven't rotted,until cuttings root sometimes they drop leaves as there aren't any roots to support the new growth.Figs can be fiddly,too much humidity and the wood can rot and the leaves will droop, not enough and the leaves can droop lol.Mould,fungus or bacteria can also wreak havoc.
For that reason I use horticultural grade perlite and CocoCoir as both are quite sterile.I started out with just adding some perlite,experimented with 100% perlite but settled on roughly 50/50 mix.It really depends on a number of factors what mix will work for you-how damp the coir or compost is(I don't use as it's got too much bacteria and fungus potential) is,how fine the perlite,how well draining the pots or cups are,whether you add air holes on the sides as well as the bottom,whether you use a bottom heat mat or some other source(I use the radiator),whether you use lights(I don't),how humid you allow the box to get(humid is good,sitting water is not) -there's no magic formula because everyone has slightly different methods and environment,I'm sure you will settle on what works best for you.
If you are confident that the woood hasn't rotted I would disinfect them,either with a weak bleach solution or something else, use clean cups with holes for air and drainage on the bottom and side,a lighted more high perlite mix and put them back in a humidity bin(as this is your chosen method).I would probably give the box a clean as well with some disinfectant or something to be safe.
If all he above fails i blame the cuttings lol.
This may all sound a bit surgical,I have also had success just sticking the cuttings in a pot outside in summer,but inside we create a perfect environment for problems unless we're careful-wood and soil for organic matter,bacteria and fungus+warmth+humidity.I learnt the hard way,now I try to keep everything as sterile as possible.
My No.1 tip,find local trees if you can,take cuttings,kill as many as you have to to get your method perfected