the problem is on the real amiga floppy or at the .adf file you use to install the amigaos cd on uae?
with floppys is common place a long time now, don't forget that the disk drives we use are more than 10 years old! the one from my 3000 is 15 or 16! it's amazing that after all these years it works most of the times!
and the floppys of today are not so good as the old ones i can tell you for sure. just preper on a real amiga a new emergency. every time a make one,i update the files of emergency disk with the latest version of the bb2, they leave about 2kb free to the disk at the end!