There could be a lot of reasons why your having this problem, make sure anti-virus software is not touching the folders where the .PGO, .shared, and .meta files are located. What entries are you finding in the Event log?
Has anything changed on the Server that maybe affecting QV?
You're right for the Extension error is a bug for V11 RS1, but this error will not caused your QVS service to fail.
Meanwhile, as for V11 SR1 you need to take more care for a setting called "Link Machine Name" as it will cause your documents (application) accessing issue. Yet this setting can only be changed through editing the config file directly (you can't change it on QVMC due to application bugs).