Default "SD" files not synced with files seen on PC

So I've tried looking for more info on this issue I'm having but, no luck.
I notice that when I plug my Nexus 5 to my PCs (Doesn't seem to matter whether it's work or home) on Windows 7, I see older versions of files, newer files do not exist, etc.
One example I have is there is a save file from Retro Arch that when I check the file through ES File explorer it's dated 2/19 (the last date the file was written) and when I look in windows, the file is dated 2/16.
Just to verify that it's not just a system date issue, I have opened both files on an emulator on PC and they are in fact different. The file from the 16th is an older version of that save file.
The only way I can get the current file is if I use ES File explorer and copy via local lan.

This gets real annoying when I have a new file that I would like to transfer, say a work file that I put on the download folder, I go to open it on my home PC and it does not exist yet I can see it in ES file explorer.

Is anyone else experiencing this? Any tips on how to resolve?

I'm running stock, no root, Dalvik. Nothing special.
Thanks!