WBPP doesn't handle my dark frames like BPP

[Seldom]

I ran a series of exposures last night: Lum(30s), Red Green Blue(all 120s), Ha SII OIII (all 240s).  Since I needed three different Master Darks, I ran WBPP three times.  But when I was done I noticed that Dark Current gradients from WBPP were much worse on my narrowband images.  I then ran BPP with the same settings as WBPP and  the Dark Current gradients disappeared.  I also noticed that the alignment on my BPP was much better (I selected an image to align on) than the alignment from WBPP.  Doing things the old way has fixed my problem, but is there a way to fix it with WBPP?

[Seldom]

Apologgies if this shows twice: First copy disappeared when I tried to add an image

I ran a series of exposures last night: Lum(30s), Red Green Blue(all 120s), Ha SII OIII (all 240s).  Since I needed three different Master Darks, I ran WBPP three times.  But when I was done I noticed that Dark Current gradients from WBPP were much worse on my narrowband images.  I then ran BPP with the same settings as WBPP and  the Dark Current gradients disappeared.  I also noticed that the alignment on my BPP was much better (I selected an image to align on) than the alignment from WBPP.  Doing things the old way has fixed my problem, but is there a way to fix it with WBPP?