Hi,
I'll recomend you to debug saving process. I have 2 ideas what can cause it:
1. Transaction rollbacked by some reason by mysql and magento don't know about it.
2. One of third party extension change product saving and you don't see error of saving.
Take a look in magento logs(system and exception ) and let me know if you see anything there. To help you more access to the magento/server required(write me PM if you can provide it).
Kind Regards,
Art Malkovich - Onilab