Sounds like "box nails", in which case if you try to set them and putty, your putty will most likely pop. Besides they can be a hassle trying to set. IMO they should be pulled.
Now I know Ken & Keith usually frown on this type of thing, but they know I'm not a spammer. I'm a "Forum Loyal", and this will solve your problems
(This tool's amaizing for lifting those nails out)
http://cgi.ebay.com/ws/eBayISAPI.dll?Vi ... RK:MESE:IT( This will take care of the squeeks )
http://cgi.ebay.com/HARDWOOD-FLOORING-S ... 1c1207f6b9