Why are my kallisto and salmon results differing so much just for lncRNA transcripts?
There has been a detailed comparison of kallisto and salmon for lncRNA transcripts by Zheng et al https://www.biorxiv.org/content/biorxiv/early/2018/01/09/241869.full.pdf

It shows them to be near identical. This suggests there is some problem with the way you made the comparison/plot.