This happened to my 1999 XK8 and hope this helps.
Recently I installed the by pass caps for the front latch
hoses until I can afford the time to replace these hoses and
still be able to use the top for the limited sunny days we
have here in North Eastern Pennsylvania. Being used to the
Boxster and just pushing the button, I made a slight mistake
and started putting the top up whilst the cap was still on.
Once I realized what I had done I quickly pressed the down
button and removed the cap. Not the fun begins. I was able
to get the top up but the rear windows would not go up and
the (convertible latch not closed) message appeared. I tried
to put the top back down and NOTHING.. NO motor noise. no
activity, All fuses checked ok. I said a few words that even
the devil himself would have blushed. After reading many on
line remedies. I checked the pump fluid and it was quite
low. I guess after all the loss of fluid from the front
latch being bad. I topped off the pump tank and then the top
started working up and down again. This leads me to think
that there is a low level fluid sensor that makes the pump
inoperable(maybe). Witht the top down and the front latch
manually closed the (convertible latch not closed)
disappeared. Now I put the top back up, rear windows still
won't move. I manually close the front latch and the
(Convertible latch not closed appears again. I did this
cycle several times to see if this may reset the BPM or
SLCU. NOPE still the same thing. Now I jumped both the rear
window relays to close the windows. At least the rain won't
get in now. Then a light bulb went off in my head. Let's see
if it works now. I manually open the front latch. The front
windows go down a bit like they should, the rear windows go
down and the top operates as normal. Crossing my fingers, I
pushed the close button and then manually close the front
latch. Viola The rear windows went up. My guess is that by
jumping the rear windows to bring them back into position,
reset the BPM and other bits so there was no confusion. I
hope this helps anyone who has had this problem. Another
note. Last week I found a strange wet spot in the forward
section of the rear left wheel well. Guess what, The rear
ram hose shows signs of wear and leaked fluid out as well. I
love getting intimate with our fleet and by the time I fix
all these little problems, I should open my own shop LOL.
Thank you for this web site. It has helped and I hope this
post helps others.

 

The only reason your windows went up is because you filled the tank that allowed the rams to fully extend so it could trip the switch that tells the security module to close the windows.