Do you think a new installation with fat /boot filesystem could solve the problem ? (except buggy USB u-boot boot support)
Maybe I could only do mkimage manually on fat /boot partition
Never worked for me, I'm afraid - but I think it was more an issue with talking to the usb devices properly than an issue with the fat support. Not sure, though, didn't spend much time on it.
Other thing:
Can I keep in NAND both uImage/uInitrd for HDD and NAND distros ?
I want to keep default guruplug-lenny on NAND and squeeze on HDD.
No, doubt that. But you could copy the modules from the NAND to your hdd/sdcard and just use the same Kernel and initrd for both. That *might* work - there is no warranty that it does, though.
Or copy the system from the NAND to a different partition/sdcard, then you have space in the NAND for more kernels...