I took a quick look at the two XISF files on my laptop and didn't see anything obviously wrong? I'll take a closer look on a better screen tonight.
How large are the spots? If they are caused by cold pixels you could run CosmeticCorrection with Autodectect on the subs before integrating. I can't think of any obvious reason why you'd get cold pixels in LRGB/Sii/Oiii and not Ha though...
Cheers,
Rick.