I am very happy to read your post, because I have the same problem. In the beginning I was using FileMaker 11 advanced as well, strangely here I did not have this issue. Now I am running my database on FileMaker 11 server (newest version). now I am not able to see all the records in the SQL table although I know all records are there. For example when there are 500 records I can see them for a part of the second and then I can only see a small part of them (70 or 30). when I refresh the window I am always just able to see exactly 6 records. I thought maybe this is the issue of the SQL driver that I am using? (Open source driver from actual technologies).
Were you able to solve this problem? I would be very happy for any advise.