My first guess would be that the data structure itself (resp. the interaction with Storable) is at fault. So instead of using Storable, maybe dump it using Data::Dumper, and then try to read/eval it in a separate program and use Storable in the separate program to store it. If using Data::Dumper makes the problem go away, and using Storable in the separate program makes the error reappear, everything is well. Otherwise, you have to subdivide the program and modules further...