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Should point out that if you can't reproduce exactly the results using the same algorithm in a different program, then one of the bits of software has a bug. There is no flexibility in the implementation.
There is unlikely to be any difference in the actual bit of code (I still call them subroutines!) doing either the Lanczos resampling, or the bilinear spline: in fact I'll bet they've been lifted straight out of either Lapack, the Naval Surface Warfare library, or Numerical Recipies. The maths should be identical and reproducible. As for stacking, it's not a very complicated algorithm. However, I wonder if gains might be made by weighting the contribution to a final pixel from individual subframes in the summation by the FWHM values in each, or some similar data quality metric?
The real gains from one bit of software to the next will be in optimising the rejection criteria in the stack for your data. The optimal parameters will depend on the type of noise and its particular realisation that you're trying to stack out.
cheers,
Andrew.
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