Greetings everyone!
I have been using Inkscape to make multiple pages from the same file via the layer feature and something that was causing me issue / frustrating the bajesus out of me, was every now and then I was unable to initiate a selection box or deselect an object by clicking the white space.
To cut a long story short, it turns out Inkscape was still detecting objects in the layer below despite it being hidden! So if you are using Inkscape in this way be sure to use the lock feature when you hide a layer and this will stop Inkscape from attempting to select something it can't see.
Hope this helps!
- Bruce