Are SNPs always in linkage disequilibrium with other SNPs
There can be a number of reasons for Linkage Disequilibriunm (LD). Here is a non-exhaustive (non-referenced also) list.


Random LD happens
Epistasis
A recent selective sweep
Hybridization
Population structure
Genetic drift can also create negative LD (see Barton and Otto, 2005)


Of course, in all cases, reduced recombination rate will help to create an LD and to retain it for a longer period of time.