Please add link to core issue(s) on your module frontpage. Maybe we can find the root causes.

As I participated with #1284364: Use variable_initialize() against broken values - Notice: unserialize() [function.unserialize]: I'm curious about what causes the faulty variable values.

Could you suggest your users to add comments to #1284364: Use variable_initialize() against broken values - Notice: unserialize() [function.unserialize]: telling what variables are in err.