Could be a few things. First off I would send a fecal to the vet to make sure coccidia or other parasites haven't started up. Since you mentioned she was treated recently, did you give her a probiotic after the treatments? Her lack of eating and listfulness could be due to an imbalance in her gut since the coccidia treatments would have killed off alot of beneficial gut flora as well. Doing a search on 'probiotics' in the forum here should bring up threads listing names of common products used for reptiles, drawing a mental blank right on what the common one used here is called.
Though your dragon's haven't mated yet I would still recommend giving them their own cage. The male could be stressing her out, hence why she had coccidia flare up before. Also, never good to leave a lay box in there all the time as they quickly dry out. The soil should remain moist and easy to pack, so when the female does dig a tunnel it won't collapse on her. Also, are you really ready for the cost, care and responsibility of 60-100 or more baby beardies?
What are the basking temperatures in the tank? How long is the lighting on? Hiding under her log etc may be a sign she is getting ready to burmate. However before I would let her do that, I would take the steps mentioned above first.