Ignored Files: rejecting until file info is updated

[binarybana]

So I have ".git" in my .SyncIgnore on all my machines, and have had it this way for quite some time, but I've noticed that over time the machines will come 'off sync' and eventually get some files that don't sync (although normal files continue to sync fine). Logs on all machines have entries similar to:

[20130718 23:40:15.126] State sync finished for folder /home/bana/GSP
[20130718 23:40:15.222] LoadTorrent: requesting to load file research/samc/class-paper/.git/refs/heads/master which is modified on disk (cur:1376584154 stored:1376583655) - rejecting until file info is updated
[20130718 23:40:15.222] LoadTorrent: requesting to load file research/samc/class-paper/.git/logs/refs/heads/master which is modified on disk (cur:1376584154 stored:1376583655) - rejecting until file info is updated
[20130718 23:40:16.053] LoadTorrent: requesting to load file research/samc/class-paper/.git/COMMIT_EDITMSG which is modified on disk (cur:1376598521 stored:1376679206) - rejecting until file info is updated
[20130718 23:40:16.054] LoadTorrent: requesting to load file research/samc/class-paper/.git/index which is modified on disk (cur:1376598521 stored:1376679206) - rejecting until file info is updated

I realize I could delete the entry in btsync, re-add and this would go away for a while, but then it would probably come back (as it has in the past). Anyone have ideas for a permanent fix? I can generate the full scale logs for what I see right now, but catching it 'in the wild' upon first appearance might be harder.

*Edit* I forgot to mention that these are all Linux x64 with btsync 1.1.48.