Optiplex 3010 bios issues

I cant seem to update the bios beyond A09. I do not get any errors but it does not change after update. It has some other issues too such as only seeing 2 SATA devices unless I use command and configure to reactivate the other ports. I run the update from a cmd prompt and create a log file which gives no errors but does have no system manifest found under the info for the current bios version. At the end of the log file it says exit code 2 need to reboot to continue. Now for some extra info. The harddrive has been changed and there is only a single partition. Im not sure if that has something to do with it for example if its looking for some Dell files that it cant find ? I have also doe this from freedos booting from a USB and it does the same thing. It acts like it works but then reboots, messes up my SATA settings where I dont have a CD drive again, have to run the CC files in windows to fix that and reboot again to have CD. 

I guess my question is are there any others ways to update or flash the bios ?