I have the problem as well on my netbook (Asus eeePC 1000H) running Ubuntu 10.10.

My wireless card reports negative values for the signal level for "bad" APs and positiv values for the good AP. As the noise value is not reported (noise == 0) the quality of all signals is considered as maximal.

At the moment I think that the network manager, either consider quality instead of signal level to choose an AP or that it has problems with the mixing of negative and positive values.
As those values comes from the driver, I think the easiest way is to fix the network manager to handle this situation correctly.

Here is some example output from iwlist scan. The network manager tries to connect to the AP with MAC addr 00:03:52:29:62:43,  which is actually the worst one considering the signal level.

          Cell 01 - Address: 00:03:52:29:62:43
                    Channel:9
                    Frequency:2.452 GHz (Channel 9)
                    Quality=70/70  Signal level=-188 dBm  
                    Encryption key:on
                    ESSID:"eduroam"
                    Bit Rates:1 Mb/s; 2 Mb/s; 5.5 Mb/s; 11 Mb/s; 6 Mb/s
                              9 Mb/s; 12 Mb/s; 18 Mb/s
                    Bit Rates:24 Mb/s; 36 Mb/s; 48 Mb/s; 54 Mb/s
                    Mode:Master
                    Extra:tsf=000000086a538af7
                    Extra: Last beacon: 16ms ago
                    IE: Unknown: 0007656475726F616D
                    IE: Unknown: 010882848B960C121824
                    IE: Unknown: 030109
                    IE: Unknown: 2A0100
--
          Cell 12 - Address: 00:03:52:1C:18:43
                    Channel:9
                    Frequency:2.452 GHz (Channel 9)
                    Quality=70/70  Signal level=50 dBm  
                    Encryption key:on
                    ESSID:"eduroam"
                    Bit Rates:1 Mb/s; 2 Mb/s; 5.5 Mb/s; 11 Mb/s; 6 Mb/s
                              9 Mb/s; 12 Mb/s; 18 Mb/s
                    Bit Rates:24 Mb/s; 36 Mb/s; 48 Mb/s; 54 Mb/s
                    Mode:Master
                    Extra:tsf=00000008848ace68
                    Extra: Last beacon: 460ms ago
                    IE: Unknown: 0007656475726F616D
                    IE: Unknown: 010882848B960C121824
                    IE: Unknown: 030109
                    IE: Unknown: 2A0100
--
          Cell 16 - Address: 00:03:52:1B:F5:03
                    Channel:9
                    Frequency:2.452 GHz (Channel 9)
                    Quality=70/70  Signal level=-182 dBm  
                    Encryption key:on
                    ESSID:"eduroam"
                    Bit Rates:1 Mb/s; 2 Mb/s; 5.5 Mb/s; 11 Mb/s; 6 Mb/s
                              9 Mb/s; 12 Mb/s; 18 Mb/s
                    Bit Rates:24 Mb/s; 36 Mb/s; 48 Mb/s; 54 Mb/s
                    Mode:Master
                    Extra:tsf=000000090231fecc
                    Extra: Last beacon: 1168ms ago
                    IE: Unknown: 0007656475726F616D
                    IE: Unknown: 010882848B960C121824
                    IE: Unknown: 030109
                    IE: Unknown: 050400010000
--
          Cell 18 - Address: 00:03:52:1C:32:93
                    Channel:9
                    Frequency:2.452 GHz (Channel 9)
                    Quality=70/70  Signal level=-182 dBm  
                    Encryption key:on
                    ESSID:"eduroam"
                    Bit Rates:1 Mb/s; 2 Mb/s; 5.5 Mb/s; 11 Mb/s; 6 Mb/s
                              9 Mb/s; 12 Mb/s; 18 Mb/s
                    Bit Rates:24 Mb/s; 36 Mb/s; 48 Mb/s; 54 Mb/s
                    Mode:Master
                    Extra:tsf=000000089c363177
                    Extra: Last beacon: 536ms ago
                    IE: Unknown: 0007656475726F616D
                    IE: Unknown: 010882848B960C121824
                    IE: Unknown: 030109
                    IE: Unknown: 050400010000
--
          Cell 21 - Address: 00:03:52:1C:24:43
                    Channel:9
                    Frequency:2.452 GHz (Channel 9)
                    Quality=70/70  Signal level=-181 dBm  
                    Encryption key:on
                    ESSID:"eduroam"
                    Bit Rates:1 Mb/s; 2 Mb/s; 5.5 Mb/s; 11 Mb/s; 6 Mb/s
                              9 Mb/s; 12 Mb/s; 18 Mb/s
                    Bit Rates:24 Mb/s; 36 Mb/s; 48 Mb/s; 54 Mb/s
                    Mode:Master
                    Extra:tsf=00000008783cd417
                    Extra: Last beacon: 548ms ago
                    IE: Unknown: 0007656475726F616D
                    IE: Unknown: 010882848B960C121824
                    IE: Unknown: 030109
                    IE: Unknown: 050400010000
--
          Cell 25 - Address: 00:03:52:1C:08:C3
                    Channel:13
                    Frequency:2.472 GHz (Channel 13)
                    Quality=70/70  Signal level=-183 dBm  
                    Encryption key:on
                    ESSID:"eduroam"
                    Bit Rates:1 Mb/s; 2 Mb/s; 5.5 Mb/s; 11 Mb/s; 6 Mb/s
                              9 Mb/s; 12 Mb/s; 18 Mb/s
                    Bit Rates:24 Mb/s; 36 Mb/s; 48 Mb/s; 54 Mb/s
                    Mode:Master
                    Extra:tsf=000000087d525e68