Question: "What are the chrNrandom[table] files in the human assembly? Why are they called random? Is there something biologically random about the sequence in these tables or are they just not placed within their given chromosomes?"
Response: In the past, these tables contained data related to sequence that is known to be in a particular chromosome, but could not be reliably ordered within the current sequence.
Starting with the April 2003 human assembly, these tables also include data for sequence that is not in a finished state, but whose location in the chromosome is known, in addition to the unordered sequence. Because this sequence is not quite finished, it could not be included in the main "finished" ordered and oriented section of the chromosome.
Also, in a very few cases in the April 2003 assembly, the random files contain data related to sequence for alternative haplotypes. This is present primarily in chr6, where we have included two alternative versions of the MHC region in chr6random. There are a few clones in other chromosomes that also correspond to a different haplotype. Because the primary reference sequence can only display a single haplotype, these alternatives were included in random files. In subsequent assemblies, these regions have been moved into separate files (e.g. chr6hla_hap1).
In my experience working with PLINK, the SNP data are annotated with rsid, and not chromosome/position. In that case, I cannot imagine that these contigs will have rsids associated with variant positions. What is the documentation you are referring to?