How to use Compact Flash in eCos?

One other important thing to be aware of is that the compact flash and LCD share pins on the Nios II development boards. If you want to access compact flash, you need to ensure that the LCD is not connected to the board. It doesn't sound like this is your problem, since you were able to access the compact flash using other software.

To help debug the problem, you could enable the debug macros in altera_avalon_cf.c and disk.c. The information these produce may help shed light on the problem.

I wouldn't expect JFFS2 to cause any issues. However to be certain that it's not something like that which is causing things to come unstuck, I'd recommend that you create a new project in configtool and follow the steps outlined in the getting stated guide, i.e. just add in the packages listed there. Hopefully that'll get you to a working system, and help you diagnose the problem that you've currently got.