We also agree and found the problem now. Since we build everything (MIDAS Event Header, Bank Header, Banks etc.) in the FPGA we had some struggle with the MIDAS data format (http://lmu.web.psi.ch/docu/manuals/bulk_manuals/software/midas195/html/AppendixA.html). We thought that only the MIDAS Event needs to be aligned to 64 bit but as it turned out also the bank data (Stefan updated the wiki page already) needs to be aligned. Since we are using the BANK32 it was a bit unclear for us since the bank header is not 64 bit aligned. But we managed this now by adding empty data and the system is running now.

Our setup looks like this:

Software:
- mfe.cxx multithread equipment
- mfe readout thread grabs pointer from dma ring buffer 
- since the dma buffer is volatile we do copy_n for transforming the data to MIDAS 
- the data is already in the MIDAS format so done from our side :)
- mfe readout thread increments the ring buffer
- mfe main thread grabs events from ring buffer, sends them to the mserver

Firmware:
- Arria 10 development board
- Altera PCIe block
- Own DMA engine since we are doing burst writing DMA with PCIe 3.0. 
- Own device driver
- no interrupts 

If you have more questions fell free to ask.