Bad transfer speed after Firmware upgrade

You need Cat5e or higher. Cat5 isn't good enough.

Even if you haven't touched your hardware it's still possible to have a coincidental problem and a good idea to try to rule that out. I would suggest trying what I suggested above.

You could try installing your addons over the top of themselves and see if this makes a difference. It has been known to make a difference sometimes.

I believe your disks aren't on the HCL. Disks not on the compatibility list may/may not work. It's possible a firmware update could cause issues with disks that are not approved for use with the ReadyNAS.

Edit: Checking for a bad disk using the "Disk Test" boot option using the boot menu (http://www.readynas.com/kb/faq/boot/how_do_i_use_the_boot_menu) could also be a good idea (I would try this after other suggestions)