> How u-boot can write to the chip?
U-Boot can do anything it wants to.
U-Boot can usually be set up to load code over the network, so U-Boot usually has Ethernet driver code in it.
The MCF5485 has a "FEC" (Fast Ethernet Controller) module. Search the U-Boot source for code that writes to the "PALR" and "PAHR" registers.
I don't have your copy of U-Boot set up the way it is for you. I don't want a copy (don't post or send). Look in the U-Boot "cpu" directory. Find a directory in there that matches your chip. Look in there for a file called "fec.c' or a name close to that. Read it.
By mixing and matching you have a custom build that nobody else can support but you.
You should find out why the old one doesn't work on the new boards and change the old one so it works on all boards, or find out why the new one is unstable and fix it. Your mixed setup is unsupportable and can't be updated in the future.
What are the differences between Revs A, B and C? Have you looked for code or documentation on the differences? Have you compared the old and new u-Boot sources to see what changed? There may be a small bit of code in the new one that supports later revs you can copy into the older one.
> Further debugging is impossible.
Debugging is never impossible. There's always a way. It may take months of work, but it isn't "impossible". SIMPLIFY the system. Remove features and drivers until it is stable, then put them back until it fails. Remove your Application code. it may be triggering the problem.
If you don't want to read and understand the U-Boot and Linux code to find out what is wrong, you'll just have to wait and see if you get an answer here. If nobody else has your mixed setup, then there's nobody to help you anywhere.
There's another problem. A particular version of U-Boot sets up the hardware (writes to controller registers0 for the version of Linux.it was shipped with.There may be parts that have to match between them, and the old and new ones ARE different because the MAC-address setting isn't working when you mix and match. There may be other ptoblems you haven't noticed yet.
That's why your "new u-boot and old linux" is a bad idea.
Tom