From what I saw on your post on pouet.net, it does not work with CosmosEx but works with HxC ?
I though the problem with my FDC routine was not to manage CRC / RNF errors but it would be surprising this kind of error happen with emulators ?! Or maybe a problem with speed ? Is the CosmosEx slower than the HxC ?
This just might need a test with the latest firmware. There was a major fix for floppy issues on 2016-01-17, and that issue was reported more than half year before that, so it might be already fixed. So, anyone wants to test it now?