I had exactly this problem and managed to solve the issue, (Win7 64bit) . The box refered to is simply not there, most frustrating
The support team were in fact not 100miles off when they refered to screen size. WIthin the options widow where you have the checkboxes, it seems they are not visible as they are hidden and cut off by the window size.
Solution: use the keywoard "Tab" and "Space" keys to navigate and activate the checkboxes. You are shooting in the dark slightly but it is fairly intuatiive if you are accustomed to navigating with a keyboard.
I managed to set the required permissions and submit successfully to HMRC.
This was the "answer" I got from HMRC help desk - use the tab and space key. However when I tried following their direction over the phone I could not get it to work! As it was over 3 weeks ago now, I can not remember the exact key sequences they advised. I assume you would need to have your cursor within the window and on the first visible check box, then tab (to the next box) and hit space to insert the check mark etc. is that how it works? In any event the actual PDF from HMRC is wrong as they have still not updated the CT rates for financial year commencing April 2011, which was reduced to 20% - they are still calculating on the old rate of 21% which would mean you are paying too much tax!! I pointed this out at the same time I alerted them to the Adobe issue, and they advise they did not plant to post a new (correct!!) PDF until OCTOBER 2011 - so right now I am in no hurry to submit; by that time perhaps Adobe will have rolled out a fix for this incompatibility!!