Hi,
I know if you use a VS website creation project (can't create VS DB projects with the version I have - Standard), you can create a dataconnection and view the connection string. I figure if you can look at a connection string, it could give you a clue as to where the problem lies. If you can't create a dataconnection, then my guess it's a authentication/authorization/permissions problem. When you access the DBs with SQL Server MS, you are likely signed on as the same person that installed the manager - and have full access. Are you suing the same identity and sign on when you are using VS? Also, you have options for authentication with SQL Server: windows or sql server native (and I think 'mixed' mode). If you are using windows authentication, it will use your windows login info for access to the server; if you are using sql server native authentication, you'll see a place to enter a user name and PW.
If you look at the server browser, which widows servers does it show, just the local, or network as well? If you can get to the box that has the SQL Server instance, you're at least part of the way there. If you can't get that, I'd guess authentication problems. If you get to the instance but can't connect, then it's more likely an authorization issue.
Go back to the management studio and take a look at the properties for the server instance and the databases you are trying to access via VS. Take a look at the properties/security item for the instance, and the properties/permissions item for the DBs. You might see something there that will show you where the problem lies.
I do know you'll need to use ASPNET_REGSQL.EXE to access the aspnetdb, even if you created that already using the management suite. I guess you might also need to ASPNET_REGIIS, if you are using IIS as the webserver in your VS projects (but I doubt that would not allow you to see the SQL Servers).
Anyway, some stuff to try. Good luck. BRN..