"ls $PWD" and "ls ." get different files, strange caching perhaps?

I have a strange problem on my Linux Mint machine (with solid-state drive if that matters). Somehow the machine (on multiple occasions) gets *different* files, and different content for the same file, if I do "ls $PWD" instead of "ls ." or just "ls". That means I can write the file into the present working directory and pick up something different copying it from another directory. It's not $PWD set to the wrong thing, I can hand-type the directory name. I've checked this pretty carefully, but it does come and go. That makes it hard to make and to test production scripts and code. adam@RADIUM:/home/adam/cd2/adam_dev/rsim ==> ls . ClearPrice.cme Makefile.win data gfiles rsim5.tmp src zlib ClearPrice.src ReadMe.txt err include rsimdone.txt tools Makefile build g2f out scripts vs2013 adam@RADIUM:/home/adam/cd2/adam_dev/rsim ==> adam@RADIUM:/home/adam/cd2/adam_dev/rsim ==> echo $PWD /home/adam/cd2/adam_dev/rsim adam@RADIUM:/home/adam/cd2/adam_dev/rsim ==> ls $PWD ClearPrice.cmd Makefile.win err include scripts vs2013 ClearPrice.src ReadMe.txt g2f out src zlib Makefile build gfiles rsimdone.txt tools adam@RADIUM:/home/adam/cd2/adam_dev/rsim ==>