I recently installed CRM 3.0 for a long time client. He's been bothered ever since with the issue of the Settings area disappearing from the web client when he has Outlook open. He is running the desktop client. I understand this has been a problem for some for awhile. Actually our problem also included Calendar disappearing from under My Work in Workplace. Ben Vollmer wrote a great blog describing how to fix this. However, it didn't seem to work. Basically Ben recommends changing the ServerURL registry value to a different one from that used by the web client. For instance if you use http://server:5555 to access CRM, change this to http://192.168.16.2:5555 in the registry (this being the IP of the server). I'll let you read Ben's blog for more info. However, that didn't seem to work in this case. We are running V3C and Update Rollup 2. I noticed there is one more registry value at the bottom of the list, WebAppUrl. I changed this from http://server:5555 to http://192.168.16.2:5555 as well and this seems to have fixed the issue. Don't know if just changing the WebAppUrl would have done it but changing both did so I'm leaving well enough alone.
PS - Well I wrote that yesterday and today I was at another client's and we installed the Outlook Desktop client and had the same problem. I was able to just change only the WebAppUrl value and it worked great. I also believe that this is peculiar to the Desktop client. I use the Laptop Client and have not had that issue.