Why is the judge holding the file if the sentence was served?

My wife is currently serving a sentence for "conspiracy"(FCI Tallahassee). However, a prior conviction for "failure to appear" (in TN)is causing problems for her at the federal level. In a nutshell, there is an issue between the bonding company and general sessions court judge(Bristol, TN). She has already served the sentence for the failure to appear charge in TN. But, the judge will not "clear" the case and "sign off" on the file because of some issue between him and the bonding company. We cannot get a straight answer as to why this is happening. I fear that something "shady" is going on, and our lawyer won't even give us an answer. What could possibly be going on behind the scenes that would make the judge "ignore" her case? It is ultimately adding a year to her sentence! The warrant officer in TN says the case was "cleared" from his computer months ago, but remains on the judge's desk. The judge initially said that he "would take care of the matter", but nothing has been done. Can you give me any idea as to why this might happen? What could possibly be going on between the judge and bonding company? Thank you.