I have recently upgraded to Oracle APEX 5 and had a strange issue with some of the inputs not being selected.
I narrowed it down to controls that were nested within a label.
It seems that if there is no 'for' attribute and 'id' on the control it fails.
//This will not check the input
<label><input type="checkbox"><span>This is a test</span></label>
so I can manually change it to this to prove it works.
<label for="chkTest"><input id="chkTest" type="checkbox"><span>This is a test</span></label>
However if you save the above html into a file and load it , both will work.
I then noticed in some older apps in apex 4 the inputs work and they are simply wrapped in a label element....