It's always been like this since the intro of the PDF filter. That's why Mike, who answered your question above, uses Pantone books to check colours, that's why when I was working I used a restricted palette of colours that I knew. Both of us relied heavily on Adobe Acro Pro so that we can check to see what the output was and do something about it. Also both of us use a higher quality of monitor and we regularly check its performance. I don't know what Mike uses but I used ColorVision Spyder2 which I don't know if its made now. Yes it's all the darker colours that cause the real problems, the maroons and dark greens can look really muddy as well as you found out the darker browns.

You have to get yourself a reference and if you don't want to spend £200 on a pantone book then make yourself up an A3 sheet with what you think is a reasonable selection of colours that you use with colour value labels along side with both RGB & CMYK stated. Even if you had Illustrator on your H/drive you still would have some problems with the difficult colour maybe not as bad as in Xara but still there. If you are going to do printed work more than once a month I would also recommend a 2nd hand copy of Acro Pro.