All cygwin git repos becoming corrupt on reboot

So I have a gitolite setup currently running in cygwin and everything works fine during the initial gl-setup; I can push/pull from the repositories all day long with no problem. However, the second I reboot my machine, every single repository becomes corrupt. I took pre/post reboot tars and, using kdiff, see that all of the files under the "objects" directory have changed... significantly. The files in my local cop开发者_如何学编程y (still on windows but not in cygwin) do not change however.

To give you an example of how extreme the changes are... here are the hex dumps of a random object:

Pre:

78 01 2B 29 4A 4D 55 30 33 61 30 31 00 02 85 E4  x.+)JMU03a01..…ä
FC BC 34 86 90 9D 41 31 26 67 84 8E BB 38 BD 5D  ü¼4†..A1&g„Ž»8½]
BC 48 30 55 EB C5 A2 EB B6 10 E9 EC D4 CA 94 CC  ¼H0UëÅ¢ë¶.éìÔÊ”Ì
22 86 AD DF DE D6 27 44 FC 7C FA 6D DA 89 15 7B  "†­ßÞÖ'Dü|úmÚ‰.{
37 4D EC 11 54 B9 F2 14 00 C6 66 1F 3E           7Mì.T¹ò..Æf.>

Post:

39 D5 AD B9 06 05 A0 7D 8F D2 16 F9 34 DA 62 EE  9Õ­¹.. }.Ò.ù4Úbî
21 2C D3 17 7D 35 11 4C 5E 88 58 C2 DA 09 FA C3  !,Ó.}5.L^ˆXÂÚ.úÃ
25 48 C9 07 29 A3 E3 E5 F6 7F 91 C4 29 D9 45 A3  %HÉ.)£ãåö.‘Ä)ÙE£
20 A6 07 DB 94 77 F4 7C 6D 59 E5 CC C0 08 35 91   ¦.Û”wô|mYåÌÀ.5‘
FF 22 6A 3E F5 0A 44 94 18 39 8E D0 6B           ÿ"j>õ.D”.9ŽÐk

I came across a post from git-users where somebody else had the same problem and it turns out that I'm using full-disk encryption as well (PGP Desktop) so I wonder if that's the root cause.

If anybody has any ideas, I'd be incredibly grateful!

First, it is not clear in your question if you are using yourself a full disk encryption.

Then, an anti-virus might have some unintended side-effect: deactivating it just for one reboot might be interesting to check if the problem persists.

Finally, it could be about a mount issue, as illustrated by this thread:

The problem was that the working directory from which imports and adds where done resided on a text mount. After mounting it in binary mode and starting a fresh repository, everything is fine.