Please share with us what, if any, error messages are displayed or reported. Generally, no error message usually mean operator error (you did not program the system to inject a sample from any vial; missing information; incomplete method; blank injection....).
Does the injector switch the valve? Does the sampler needle go to well plate location? Did you input a LOCATION? Does your method include the autoinjector as part of the configuration? Have you input an injection volume amount in the software. Please tell us exactly what happens when the run is initiated. This should be very simple to troubleshoot. *BTW: As you are at a University, your first step should be to discuss this with the person who helps train users in how to use the HPLC system.
Are you properly degassing your mobile phase? This sounds like it may be a flushing and priming issue. If the mobile phase is not properly degassed, cavitation, bubbles and loss of pressure will result. These will impact the A/I too.