Hi! I'm also writing my thesis with Lyx. My biggest problem is .doc template. If I open it on Libreoffice, OpenOffice or MS Office with different versions I get subtle changes in printout.
For example vertical space before image might change little and lines length differ. Then there is the typesetting in Lyx. Lyx' fonts are generally more readable than Office programs due proper kerning. Now the problem comes. What is the right layout and how I reproduce it with Lyx. If there is trick please tell to list also. Also references are different. I never learned bibtext enough to give right style of reference list. Now I have page which is list of my references and then I cross-reference to them. It is also irritating that you can't cross reference to say Fig 1 without labeling it. Or have I missed something? And last thing. I'm not professional with Lyx and I still learn a lot with it. And problems that I mentionned might not be real problems. I haven't just found solutions yet. Best regards, Hannu Vuolasaho