Yes, you are right. Conditional format currently is only supported for xls/Excel 2003 style. We are working at this very moment to do a full implementation of xlsx/Excel 2007 conditional formats (right now I was reviewing the code to draw the icon sets when you export to pdf/html).
It is a hard work because the conditional format support is very optimized for the Excel 2003 style, so the code is quite complex. For example if you insert a row into a block formatted with some conditional format with some different one, we need to split the range of conditional formatting in 3. There is a lot of stuff like this handled really well for Excel2003 cond fmt, but we need to review everything for Excel2007, because it completely changed the way it works. You can now for example have overlapping block of conditional formats, which you couldn't before, and that the old FlexCel engine made a great work of mixing them. Now we can't mix them anymore.
Excel 2007/xlsx conditional format support will be released for next version, FlexCel 6.7. I can't give a timeframe yet, but we are fully at work to make this ready as soon as we can.