You're no alone David.
This happens to me on about 1 in 10 start-ups.
It's never bothered me so I've never thought to try and track it down.
Hopefully someone else has...

---

On some (but not all) occasions when starting windows BOINC puts a BOIN manager window in my task bar in addition to the little BOINC thing in the system tray.

The only way I've found to get rid of this is to open BOINC from the system tray and then close it (using the x at the top right and not by selecting exit as the later turns of BOINC).

Clicking on the task bar BOINC does nothing. Right clicking on it and selecting close does nothing.

Admittedly it only takes an extra second or two to sort this out but is is an irritating feature and not one that the old SETI@Home system had.