If I remember correctly, this is because the Java File API doesn't let you specify the lock mode when opening a file (at least not until Java 7). So Flume ends up opening all files with a lock mode that Windows treats as "no one else can move/delete this file". The fix was to use the new API in Java 7 but I think the tail and tailDir plugins have been removed completely in Flume NG.
On Linux this isn't really a problem as the file locking semantics allow files to be moved/deleted while another process has them open. Never did fine a work around for Windows apart from restarting the Flume agent process on logrotate. Cheers, Dan