Hi,
Sorry for the issues you are having. I can help out.
If you updated 4.1 in the first 48 hours and did not go back later and change the plugin folder names, which was the cause of this then on the update to 4.1.1 it would cause the plugins to deactivate as it would change the folder names again to the correct ones.
The good news is the 4.1.1 release and after the first 48 hours of 4.1 we fixed the folder issue and this should no longer be a problem going forward now they are back to normal for you.
If you continue to have issues on a future update please let us know so we can resolve it.
Thanks