I don't know if this can help you, but here it says that serialization in Android can be buggy with large arrays of integers. In your case, you have an array of booleans, which is an integer anyway.
I would try to make tests by stripping some of the serializable data (e.g. serializing only part of the information) to see if the problem is related to the arrays.
Also, this may be obvious, but maybe not... make sure you're not loading a file that has been saved with a different version of your object (e.g. you saved your object doing some test, then you added variables to your class, and now you're trying to de-serialize).