| | Re: Cloning of PCR product
It sounds like one of your restriction enzymes may not be working. Try digesting your plasmid with each enzyme individually, and then run a diagnostic gel to see if this linearizes the plasmid (you'll no longer see the supercoiled form if they are). If both are working, maybe try doing individual digests (i.e. digest with HindIII, purify, then with BamHI).
Another possibility is that you are using way too much DNA. Try diluting everything 1:100, but otherwise keep everything else the same.