I have been using Toodledo for about 2 months (last 3 weeks using the iPhone app too).
This issue appears to IE 7 -- using Firefox v3 causes the calendar to appear above the task. I haven't checked other browsers.
One thing I have noticed on changing the date in a task. I have a list of around 150 tasks and if I wan't to change the date on the last task in the list -- I select the date field and the calendar pops up but it is partially off screen, when I scroll down the calendar dissapears. This affects changing the date on the bottom 5 tasks.
The simple workaround is to manually type the date which is fine.
For Info, I am using XP SP3 with IE 7.0.5730.11IS -- which I need to use at work.