When a Windows application starts up the default behaviour is to display the working in background cursor for 2 seconds (see the STARTUPINFO page on MSDN).
The following patch to app_start.C will prevent the cursor from being changed when BOINC starts a science application.
445c445,446
< //startup_info.cb = sizeof(startup_info);
--
> startup_info.cb = sizeof(startup_info);
> startup_info.dwFlags=STARTF_FORCEOFFFEEDBACK;
This change has already been applied to the CPDN controller program to prevent the cursor from being changed during post-processing (when a program is started 100+ times and was causing the cursor to flicker in a very noticeable and disconcerting fashion).