I am using the linksys spa941 with latest firmware on a couple of sites and am having the same problems.
I have very limited knowledge in the area of IP Phones so I'd be grateful of any pointers.
The problem seems to occur once a message has been left.
When the message indicator light is on the phone makes a popping / crackling noise (audible whilst sitting at the desk) then the display goes blank, then the 'initializing network' message is displayed, then the phone is OK but no message indicator is on, then the message indicator comes on and the cycle begins again.
This cycle happens every 30 seconds or so and stops when the message is listened to - until next time!
Thanks for your advice.