You might run into this problem again sometime. So just in case.....
I had a Latitude D600 (WinXP Pro SP2)that would "lose" the USB mouse connected to the D-dock/port replicator on occasion. It seemed to revolve around docks/undocks on my part, and probably incorrectly on my part.
I had to go through a series of steps of dis/re-connecting the mouse both to the notebook un-docked and/or reboots with the mouse then connected to the D-port and the problem was eventually resolved.
Apologies for lack of more detail, but I haven't had the system or dock in over a year. It was frustrating, but it turned out to be a simple fix- and from what I recall, a problem I thought I'd brought on myself by improperly docking/undocking the notebook (in a hurry).