I am working on a RP Chromatography using a Phenomenex Synergi 4u MAX-RP 80A 150x4.5mm Column. Several large peaks are being observed in the chromatogram late in the elution. I am using an 10/90 to 90/10 ACN/water gradient over the course of 20 minutes to elute our product. After the 20 minutes, the column is washed with 90% ACN for 5 minutes and re-equilibrated to 10% ACN for the remaining 5 minutes of our 30 minute run time.

The product peak appears around the 19 minute mark and approximately 10-12 smaller (but some comparably sized) peaks appear around 18-30 minutes. I have ran blanks with our mobile phase, with our methanol (for product dilution), and methanol of known purity from another lab.

This exact same procedure was followed on another HPLC using the same column, methanol, and product and these mystery peaks were not observed. These peaks are not observed when montioring the baseline so it does not appear to be impurities in the mobile phase.

These peaks appear consistantly in every injection whether product is being run or not and they do not appear to be reducing in strength. Please advise on possible culprits and procedures for treatment.

It appears to be a system problem, possibly void volume in the system. Check pump seals, detector, etc
By the way, you should extend your column equilibration for at least 5 more minutes to avoid retention time shift.

If the peaks are system specific, and appear in blanks and samples, they could be from contaminated mobile phase reservoirs, inlet lines or degasser.

But if it were contaminated mobile phase, wouldn't the peaks show up when monitoring the baseline. Also, the peaks show consistently at the same time points and at the same magnitudes. Wouldn't this suggest that it is something more than just the mobile phase?

By "monitoring the baseline", do you mean running a gradient with no injection?