Android Lollipop 5.0.1 weird partition issue

[Basit Saeed]

So a couple of hours ago, I flashed a factory image of Android 5.0.1 over 5.0, the process went smoothly, and I was managed to keep my data (by running the flash command without -w switch), I also fixed the rooting issue by auto-rooting utility by ChainFire. But, when I connected my phone to my PC as MTP and started copying a file, it would stop at an error stating Windows couldn't save the file because phone was disconnected.
Anyway, after rebooting the device in bootloader, accessing recovery, and mount it via TWRP, I could see all the older files/directories I had in the phone. I tried copying the same file and it would copy without any trouble, whatsoever.
Is it a weird partition issue in this new update or did I screw up flashing the factory image?
Your help will be highly appreciated.

 

[Rukbat]

Or are you transferring large files through a USB hub? (Most of them can't take sustained data transfer. What do you expect from a $10 device that has $15 worth of parts at retail?)