Have you checked the Chip Errata? The FEC suffers from SECF064 (early silicon), SECF067, SECF010, SECF175.
You might be suffering from:
SECF175: Simultaneous FIFO Read/Write Results in Data Corruption
- Fix Plan: Will not be fixed
- Workaround: Use TCP/IP to recover from the data corruption (doesn't apply for your problem though)
Try and make sure your FIFO pointers are aligned if you can.
Where is the "BD" documented in the Manual? Is it in the FEC, DMA or FIFO section? From the Reference Manual I can't work out in my head how the FEC works at all. The FEC chapter says that the "31.4.2.1 Receive Frame Status Word (RFSW)" is in the FIFO after the data. But that isn't the BD (although some bits from there might end up in the BD).
I've seen various "simultaneous access" bugs in hardware before. I suspect that some other asynchronous operation like handling a Transmit interrupt (or some other DMA operation) is reading or writing a controller register at the same time that the hardware is about to try and update the BD and it all goes wrong. I'd suggest keeping an in-memory circular event log, timestamped to the microsecond (or better). I suspect you'll find the "DMA Rx Interrupt" that happens on the "missed frame" happening just after some other operation where your code read or wrote a FEC, FIFO or DMA register. Look for a "time correlation" and then try to make it worse (like reading a register 20 times instead of once).
If you can characterise the problem reliably enough to recognise it, you probably have enough information to confidently work around it. If you want to report it to Freescale you may need to provide software demonstrating the problem running on their evaluation board.
Search for "MCF5485 FEC" and go through some of the other reports. Note that the MCF5485 FEC looks to be derived from the MCP5200 chip, so it would be worth reading that chip's Manual, Errata and any posts on problems with that chip too.
https://community.freescale.com/message/20009
Re: MCF5475 FEC transmit hang
MCF5485 FEC DMA problem
https://community.freescale.com/message/12666#12666
https://community.freescale.com/message/441783#441783
Re: MCF5485 FEC inverted CRC
Tom