We tried to compare PV energy to PVwatts values. They are quite different.

Most of that discrepancy is due to the fact that you are comparing AC energy output in PVWatts with DC energy output in HOMER.  PVWatts is assuming that the AC output is 80% of the DC output, so you would have to factor that 80% into your comparison.

If you are not considering the temperature effect in HOMER, that could explain much of the rest of the discrepancy.  Considering the temperature effect will tend to reduce the output.  Your PV derating factor in HOMER also makes a difference.