Solvents that are exposed to the atmosphere have the ability to absorb compressible CO2 and Oxygen. When your HPLC has low back pressure, the actual linear flow of materials could be different then when you have higher back pressure. This is due to the compressibility of air v. the compressibility of gas. This means that your HPLC results could different retention times and different peak shapes.
Also, Noisy baselines occur which can lead to very unreliable results in both quantitation and retention times. Some columns, most notably polymeric columns, do not tolerate outgassing very well.