Is your remote_hosts.cfg file up to date?

1) Normally, only one copy of BOINCMGR is allowed to run at once. But there is a command (Advanced view, Advanced menu, next to last item): "Launch another BOINC Manager". That bypasses the 'only one copy' restriction, and allows you to fill in the 'localhost:31417' that Claggy was suggesting.

2) 'GPUs have become unusable' isn't a function of the Manager: the Manager is merely reporting the status of the underlying client. With Windows 7 (or Vista), the core client can only access the GPU drivers if it is running under the same user account as the currently logged-in active user: so if you switch users, the core client loses contact with the drivers and hence with the GPU. You can get round that by shutting down the core client and restarting it in the new user context.

2/8/2012 11:49:57 AM | | GPUs have become unusable; disabling tasks
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2/8/2012 11:58:35 AM | | GPUs have become usable; enabling tasks

rem
rem cd C:\BOINC_test_data_1
start C:\BOINC_test_programs\boinc.exe --gui_rpc_port 31416 --dir C:\BOINC_test_data_1 --detach
rem
rem cd C:\BOINC_test_data_2
start C:\BOINC_test_programs\boinc.exe --gui_rpc_port 31417 --dir C:\BOINC_test_data_2 --allow_multiple_clients --detach
rem
cd C:\BOINC_test_data_1
start C:\BOINC_test_programs\boincmgr.exe /s
rem

The one thing i haven't seen mentioned is the setting up of remote_hosts.cfg with the host details, the host i was using the 2nd Boinc Installation was known as P5N-E-SLI, so that was what went in there.