have read the advice NOT to reformat the CF card since this *might* cause problems
I have formatted my cards many times. No problems other than those caused by my not being able to use fdisk and mkfs.msdos.
ohh some have reported problems with ntfs
I've never had this problem (running WinXP with an NTFS filesystem), what I have had troubles with is IE corrupting the larger of the two files (initrd.bin). Mozilla/Netscape works fine for me. YMMV.
The most important thing is to check the md5sums of the two files before you try flashing, that way you'll know that they are not corrupt. Best to check them once they are on the CF card and in your Z, that way there'll be no more copying and you can use Linux to ensure that Windows hasn't tacked on any extra file extensions (that said, I've never had any extensions stuck on - I have Explorere set to show all, etc.).