I've flashed both of my 6990's in the overclocked position using RBE & atiflash, no problems at all using Ubuntu and fglrx drivers.
I have them set to 600mhz memory, used to be 150mhz but I changed it in fear of causing damage.
Care to provide details on what you changed and how you changed it?
e.g. For the overclock BIOS on my rig I did the following:
1) With power off, set BIOS switch to overclock position on each 6990.
2) Boot to DOS on your mining rig with CD/USB/floppy (like Ultimate Boot CD) and attach media with ATIFlash.exe if not on the boot media.
3) Enumerate all cards detected with ATIFlash -i
4) Document the BIOS checksum for each of your cards with ATIFlash -cb x
where x is your adapter ID provided in step 3.
5) Dump BIOS on each adapter to USB/floppy with ATIFlash -s x BIOSx.ROM
where x is the adapter ID.
6) Remove USB/floppy and attach to a Windows PC with RBE.
7) Load each BIOSx.ROM into RBE where x is the adapter ID.
In the Clock settings tab, locate Clock info 00
(this should have GPU (MHz) = 880).
9) Modify the settings for Clock info 00
to have GPU (MHz) = 880, RAM (MHz) = 150, Voltage (V) = 1.175. (Note: Only change the RAM MHz value)
10) Modify the settings for Clock info 03
to have GPU (MHz) = 800, RAM (MHz) = 150, Voltage (V) = 1.175. (Note: Only change the RAM MHz value)
11) In the GPU registers edit VID4 (mV) from 1175 to 1050.
12) Save each BIOS image to the USB/floppy named as BIOSxNEW.ROM where x is the adapter ID.
13) Move the USB/Floppy back to your mining rig.
14) Confirm the checksum on each ROM image with ATIFlash -cf BIOSx.ROM
and compare with your previously documented values for each adapter.If and only if the checksums match proceed to the next steps
15) Flash each new BIOS onto the respective adapter with ATIFlash -p x BIOSxNEW.ROM where x is the adapter ID.
16) Once all adapter BIOS images have been flashed, reboot. It is important not to reboot until both master/slave BIOS on a card have been flashed before rebooting.
17) Boot back into Linux, and confirm the clock settings have been updated with DISPLAY=:0 aticonfig --adapter=all --odgc
18) Mine away!