I am trying to use biomart for some ID mapping between humans and mice.  I have a couple of sets of genes I'm interested in and want to bring the IDs into a common space by mapping both gene ID sets to their corresponding HGNC symbol.  

> head(human_de_geneIDs)
[1] "ENSG00000175518" "ENSG00000237075" "ENSG00000143545" "ENSG00000182118" "ENSG00000164035" "ENSG00000125355"
> head(mouse_de_geneIDs)
[1] "ENSMUSG00000017830" "ENSMUSG00000069792" "ENSMUSG00000111967" "ENSMUSG00000029371" "ENSMUSG00000018927" "ENSMUSG00000107653"

#Set up my marts for human and mouse.

mart1 = useMart("ensembl", dataset="hsapiens_gene_ensembl")

mart2 = useMart("ensembl", dataset="mmusculus_gene_ensembl")

# human / mouse id ortholog map.

orthoMap_human <- getLDS(attributes=c("ensembl_gene_id", "hgnc_symbol"), filters="ensembl_gene_id", values=human_de_geneIDs, mart=mart1, attributesL=c("ensembl_gene_id"), martL=mart2, valuesL=mouse_de_geneIDs, uniqueRows=FALSE)

orthoMap_mouse <- getLDS(attributes=c("ensembl_gene_id", "hgnc_symbol"), filters="ensembl_gene_id", values=mouse_de_geneIDs, mart=mart2, attributesL=c("ensembl_gene_id"), martL=mart1, valuesL=human_de_geneIDs, uniqueRows=FALSE)

The human orthoMap here looks like what I would expect, a human id, a hgnc symbol, and a 

> head(orthoMap_human)
   Gene.stable.ID HGNC.symbol   Gene.stable.ID.1
1 ENSG00000105976         MET ENSMUSG00000009376
2 ENSG00000142611      PRDM16 ENSMUSG00000039410
3 ENSG00000164283        ESM1 ENSMUSG00000042379
4 ENSG00000200795      RNU4-1 ENSMUSG00000096243
5 ENSG00000197506     SLC28A3 ENSMUSG00000021553
6 ENSG00000088899       LZTS3 ENSMUSG00000037703

The mouse orthoMap, however, gives only NA for HGNC symbol.

> head(orthoMap_mouse)

      Gene.stable.ID HGNC.symbol Gene.stable.ID.1
1 ENSMUSG00000091650          NA  ENSG00000128335
2 ENSMUSG00000050982          NA  ENSG00000128335
3 ENSMUSG00000063779          NA  ENSG00000134216
4 ENSMUSG00000056529          NA  ENSG00000169403
5 ENSMUSG00000040809          NA  ENSG00000134216
6 ENSMUSG00000040253          NA  ENSG00000162654

I used the exact same code to get these, I just switched mart1 and mart2 in the getLDS function.  Why does it work one direction and not the other?  Also, I'm pretty sure the first time I tried this it worked fine.  Has anyone encountered this issue before or is there possibly something i've overlooked in the code that would cause this result?  

I'm going to guess your problem is this:

https://www.genenames.org/

"HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication."

When I use the little search bar in the corner of the website with human ensembl gene IDs, I get gene names.  When I search mouse ensembl IDs, I don't.  

So "hgnc_symbol" might not return gene names for mouse ensembl gene IDs.