A new Windows App is available from our Beta Test Page.
In addition to the fixes included in 6.09 this App also uses a newer version of the BOINC API code which should fix the problem of communicating with the graphics process on Win98/ME. It might well be that some other behavior changed, too, so please test this App also if you are running a recent version of Windows.
Switching from previous Apps 6.04 - 6.09 should be painless with the included app_info.xml.
Please test and report.