Okay, you've done most of the "heavy lifting", by exonerating the column and tying the problem to one system. So, next questions:
1. The first thing to do is to verify that the flow is correct. I know you did PM on the pump, but just because I'm paranoid doesn't mean the world isn't out to get me. Try and find the "dead time" marker (t0) on your chromatograms. If that's also longer than your retention times (and especially if the percentage error is the same), then you have a flow problem.
2. If you can't find t0, then time the collection of about 10 mL of mobile phase and confirm that it's within 1% of the nominal flow.
3. Are you running premixed ("off-line") mobile phase or are you using the pumps proportioning system ("in-line")? If it's the latter (i.e., you are mixing A & B solvents in the pump) go back and re-run the "stairstep" test (
http://www.lcresources.com/resources/TSWiz/hs450.htm) to verify accurate proportioning.