I recently cleaned the carpet in one of our bedroom after our dog became quite ill. Several attempts where made with neutralizers and carpet cleaner but the odor remained, we also noticed what appear to be rust spots on the carpet. We pulled up the carpet and are in the process of replacing the pad however the subfloor nails are rusting. Is it safe to use a primer/sealer like Zinsser on the subfloor to seal the rust spots before putting the new pad and carpet back down??? Any help would be greatly appreciated

 

What you need to do is stop the rusting process not just try to block it's staining as these nails will continue to rust from now on.Your post tells me that this floor is such that exposure to water reaches these nails and now that the process has begun any future water exposure will bring more on.Zinsser is not going to stop this regardless of which of thier products you apply.

I suggest one of two directions.Either get some rusty metal primer such as Rustoleum's version or any other specifically for rusty metal primer and dab some on to the rusting nails then dab some el cheapo oil enamel on top of it (yeah I know it's labor intensive) or get one of the several versions of "rust converters" on the market which convert rust to a stable surface capable of being painted.

If these areas of rusty nails are not in an area commonly exposed to water and you replace the pad you might not have any more trouble and don't need to do anything.And you do realize that these nails will never rust enough to break free or not hold your carpeting down right? You'll be dead before it goes that far.