I had the latch hoses changed and everything seems to be working as expected now except for one problem:

When the top is up and the windows are up, and I push the button down to retract the top, the driver & passenger windows no longer go down automatically. The rear windows go down, then the top retracts.

When the windows and top are are down, and I push the button for the top to go up, it functions in a normal manner; first the top goes up, then the rear windows, then the side windows.

Does anyone know what might be causing the door windows to not roll down?

You need to reprogram the window sequence. To do this you push the window down button and hold until you hear or feel a click. Then push the window button for the window to close and hear or feel the click. This should be done when you are in the car and the door is closed. The window should operate properly by opening a slight bit when the door is opened and close when the door is closed.
This problem is often caused by a weak battery voltage. 10.5 or below they lose memory settings.

Thanks for the reply Gus however it seems to be something else causing this.

The battery was disconnected for some other maintenence performed concurrently with the hose replacement, so I reset the windows. Just to be sure, I performed the reset again just now, yet I'm still getting the same problem described above. The windows do drop slightly when the door handle is lifted, and rise when the door is closed, as they should. The battery is only a month old so I doubt if that's the problem.

That is the way mine has always worked. The windows would roll all the way down when I used the key in the door lock, however. I guess I thought it was normal.

As I understand it the driver and passenger windows stay up when the top goes down, only the rear windows drop.
They drop when the top goes up, the final action after the top latch has engaged being to raise them.

It sounds as if the shop may have reflashed the program in the memory in your Body Processor Module.

The earlier model year cars have the windows go down, and later model year cars have the windows stay up. I think the change was around 2003.

It also might be a configurable setting with the IDS dealer tool...but I do not know that for sure.

When the roof is up and you press the button inside the rear windows will go down, the front windows will drop just a bit then the roof will unlatch and retract. When operating the roof using the key in the door the front and rear windows drop all the way then the roof will retract. If this is not taking place then I would recommend closing the roof and windows and do a hard reset on your system. When you do this you may lose you radio presets.

I did a hard reset this morning, it's still doing the same thing.

FYI:
I'm sure the body processor module wasn't reflashed, this wasn't a proper shop I took it to, just a shadetree mechanic that I trust to take his time, so he doesn't have the tools to do that.

Mine is a 2003 XK8. I've had it for over a year and have had the battery disconnected several times and have reset the windows each time. Until now it has always rolled down the front windows completely using either the button or the key. Now the front windows do drop a tiny bit, they just don't roll down all the way like they used to.

Honestly - I think you may need a hard reset !!
The windows drop to clear the seals but stay up (mines a 2004)
You don't want the windows + hood down - the draught can make one spill one's champagne.

The 2006 roof operates as per what Gus stated above. I had to go out and check since I open the top with the key in the door. I had forgotten the front windows stay up when openning with rocker switch in the car.

On my MY2001 when using the console button the side windows drop just a few inches on raising or lowering the top and go back up when either cycle is complete. If I use the key in the door lock, first position is all windows down (back and side) and second position is top down.

By my manual this is the correct sequence. Maybe all the battery disconnects have set yours back to default?

Check your PM and I will provide you with my number.