To wrap it up,

I was able to program all three eeproms with original pc-bios and verify each. The pc would boot from all three of them.

The single requried change to the code was :

# svn diff
Index: jedec.c
===================================================================
--- jedec.c     (wersja 2500)
+++ jedec.c     (kopia robocza)
@@ -144,9 +144,11 @@
        /* transfer data from source to destination */
        for (i = 0; i < page_size; i++) {
                /* If the data is 0xFF, don't program it */
-               if (*src == 0xFF)
-                       continue;
-               *dst++ = *src++;
+               if (*src != 0xFF )
+                       *dst = *src;
+               dst++;
+               src++;
+
        }
 
        toggle_ready_jedec(dst - 1);

--
Thanks!
Shaddam IV