If your winter cover actually lays on the water, your cover may have some small holes or be worn enough to allow water to pass through. The weight of the cover itself on the pool coupled with any rain water on top of it will allow water to pass through any holes on the cover until there is equal foces on top of the cover as underneath. as the water on top of the cover evaporates the cover will continue to allow water to pass through until all is in equalibrium again. The best way to tell is to observe during a prolonged dry spell and see if your cover has any free standing water on it. If so, your cover is leaking.
Hope this helps.