For everyone who is interested, we discussed the issue and I think there are four possible error sources:
1. The interrupt of the FR does not work in SP 1 or earlier correct, so you will have to add a patch to the Reader.
2. Perhaps there are some TimingProblems in the Design.
3. The Frame Reader uses burst reads. So the DDR SDRAM Bridge does not support them in the configuration. Perhaps the video stream is running out of data because of this.
4. The implementation in the Nios EDS could be wrong. Perhaps the addressing of the buffer is not correct.
Would be nice if anyone could prove or dissaprove some of this issues or add to the list. Thanks.