You observe lower reproducibility as a function of pH. Consider that the compound may not be as stable as the pH increases. I have observed many compounds that degrade enough during HPLC runs that replicate injections show poor precision. Captopril, erythromycin, lovastatin, and diltiazem come to mind quickly.
Two simple experiments can identify this. Take your pick.
Assuming you are currently running at ambient temperature, lower the temperature of the sample chamber to about 5 C. If the compound is degrading, most likely the lower temperature will slow the process and increase the stability. Whether it does it enough to bring the method into usable limits is another issue.
You can also try running standard preparations (prepared at the same concentration, for convenience) in each of the different buffers over time. If the sample is stable, peak area/height will be constant over repeated injections over time. If not, you will see decrease in peak area and generally some impurity peaks will start showing up, depending on how much the molecule fragments and how well the impurities can be seen at your monitoring wavelength.
If you are going to try the formal stability study, this is best done on a PDA, where you can often see the impurities as end absorption in a 3D plot, even if your moniotring wavelength is much higher.
Other things may be causing this, but I don't think it is the presence of the HCL itself, which is immeidately separated from the parent molecule when you inject it into the chromatographic system.
Good luck!