Windows 8 (8.1) usb broken files

I use an external hard drive (NTFS) with a lot of PortableApps between 2 PCs , only these two (A and B).

I used windows 7 64x on both until recently have switched to windows 8 64x in both. Since then I have very serious problems with fundamental apps.
By connecting the disk in "A" coming from "B" gives errors when start an app ("unauthorized acess") or start apps as if it were the first time (rebuilds the configuration files).

In the worst case - Thunderbird - several mailboxes are with 0 KB.

I did a CHKDSK and it gives me several errors that are fixed but the files are blank and/or inaccessible. Supposedly they are the files that were in use when shutting down the PC but not all were being used.

Conclusion lost several mailboxes and access to other portable apps.

3 important notes:
- My PC "B" automatically turns off at "x" hours if no activity during "x" time (for energy saving and environmental reasons) but i was already using this scheme on windows 7 and has always worked well), is not a forced shutdown.
- I had a identical problem when using the "hibernate" option on my laptop and remove the disc when it was "hibernated" but that's understandable and so i stopped using hibernation.
- I switch off all kinds of suspension, disconnections or hibernation from the win 8 power schemes.

I'm also afraid that all my backups on external drives that I'm linking to these machines could be broken in future (be warned).

Anyone have this problem with windows 8? or better... have a solution to the problem