It is a known bug. Any show which has about 300 or more episodes is subject to this.
The apparent work around is to move the entire series away from PMS, update the library, empty trash, and clean bundles. After all that has completely settled, start putting them in 1 season at a time and update / let finish before adding the next. I have 450+ episodes of Modern Marvels which also exhibits this behavior. 1.0.3 has made great strides and ‘almost’ has it. A huge part of the problem was throttling from TheTVDB.