For details of binary comparsion software see comments.

Results of binary comparsion for the following bundles produce the following results :

1.5.0_06 FCS - jre-1_5_0_06-windows-i586-p.exe
>>
1.5.0_06_plus_b3 - jre-1_5_0_06-fcs-bin-b05-windows-i5860-p-03-feb-2006-s.exe

For /bin folder
---------------
2 files match exactely
65 files don't match

See attached jre5u6FCS_jre5u6+b3-s_bin_comparsion.txt for results

For /lib folder
----------------
461 files match exactely
11 files don't match

See attached jre5u6FCS_jre5u6+b3-s_lib_comparsion.txt for results.

I also compared the following bundles also:
1.5.0_06_plus_b3 - jre-1_5_0_06-fcs-bin-b05-windows-i5860-p-03-feb-2006-s.exe
>>
1.5.0_06_plus_b3 - jre-1_5_0_06-fcs-bin-b05-windows-i5860-p.exe

All files match exactely. No differences in binary comparsion of these bundles.
Manually checking the size of every file in each bundle returns the following files which are different:

Left Side: 1.5.0_06 FCS
Right Side: 1.5.0_06_plus_b3

/lib/zi/America/Indiana
Indianapolis 872 != 868
Knox 1,312 != 1,308
Marengo 904 != 900
Veray 728 != 724

/lib/deploy.jar 2,032,401 != 2,032,313
-com 1,955,011 != 1,954,923