endnote x2 on mac crashes when formatting bibliography

Fellow endnote users;

I am finishing a pHD thesis and having a nightmare. I have written my chapters separately, and when I format the bibliography for each chapter it is fine. However, when I put them together by inserting them into one single document, the “format bibliography” process only gets as far as “scanning for unformatted citations” before giving a flickering message that “word is paginating pages 48 and 49”, and then crashing a minute later, sometimes with a “COM error” message. I am at my wits end - as I say, the chapter documents individually will allow formatting but when I put them together they crash. Can you help me - I am going insane and have to hand in my thesis soon!!!