I tried changing the card and changing the PCI-e extender but the same location always fail.
I have 5 GPU connected here is some more info:
[2012-04-18 19:31:01] CL Platform 0 vendor: Advanced Micro Devices, Inc.
[2012-04-18 19:31:01] CL Platform 0 name: AMD Accelerated Parallel Processing
[2012-04-18 19:31:01] CL Platform 0 version: OpenCL 1.1 AMD-APP-SDK-v2.4 (595.10)
[2012-04-18 19:31:01] Platform 0 devices: 4
[2012-04-18 19:31:01] Failed to ADL_Adapter_ID_Get. Error -10
[2012-04-18 19:31:01] Failed to ADL_Adapter_ID_Get. Error -10
[2012-04-18 19:31:01] GPU 0 ATI Radeon HD 5800 Series hardware monitoring enabled
[2012-04-18 19:31:01] GPU 1 ATI Radeon HD 5800 Series hardware monitoring enabled
[2012-04-18 19:31:01] GPU 2 ATI Radeon HD 5700 Series hardware monitoring enabled
[2012-04-18 19:31:01] GPU 3 ATI Radeon HD 5800 Series hardware monitoring enabled
[2012-04-18 19:31:01] 4 GPU devices max detected
ubuntu@ubuntu:~/cgminer$ sudo aticonfig --lsa
* 0. 03:00.0 ATI Radeon HD 5800 Series
1. 01:00.0 ATI Radeon HD 5800 Series
2. 04:00.0 ATI Radeon HD 5800 Series
3. 05:00.0 ATI Radeon HD 5700 Series
4. 09:00.0 ATI Radeon HD 5800 Series
* - Default adapter
ubuntu@ubuntu:~/cgminer$ sudo aticonfig --adapter=all --odgt
ERROR - Get temperature failed for Adapter 0 - ATI Radeon HD 5800 Series
Adapter 1 - ATI Radeon HD 5800 Series
Sensor 0: Temperature - 48.50 C
Adapter 2 - ATI Radeon HD 5800 Series
Sensor 0: Temperature - 40.00 C
Adapter 3 - ATI Radeon HD 5700 Series
Sensor 0: Temperature - 44.00 C
Adapter 4 - ATI Radeon HD 5800 Series
Sensor 0: Temperature - 43.50 C
We can see that the problematic adapter is detected as default but desktop output is on adapter 1.
EDIT:
My flash drive hosting Xubuntu was corrupted. I tried a BAMT fresh install on a new flash drive instead and all cards are mining now.