Same bug here. It's completely annoying when making voip calls or playing FPS 
games. I did some research on this problem:
Exact every 2 minutes in syslog I get "wpa_supplicant[1112]: 
CTRL-EVENT-SCAN-RESULTS" and exactly in this moment all my wireless traffic if 
"paused" for 5-6 seconds, if I run constant ping on my access point I get:
64 bytes from 10.0.2.1: icmp_seq=7 ttl=64 time=0.540 ms
64 bytes from 10.0.2.1: icmp_seq=8 ttl=64 time=0.561 ms
64 bytes from 10.0.2.1: icmp_seq=9 ttl=64 time=6442 ms
64 bytes from 10.0.2.1: icmp_seq=10 ttl=64 time=5442 ms
64 bytes from 10.0.2.1: icmp_seq=11 ttl=64 time=4443 ms
64 bytes from 10.0.2.1: icmp_seq=12 ttl=64 time=3443 ms
64 bytes from 10.0.2.1: icmp_seq=13 ttl=64 time=2445 ms
64 bytes from 10.0.2.1: icmp_seq=14 ttl=64 time=1446 ms
64 bytes from 10.0.2.1: icmp_seq=15 ttl=64 time=447 ms
64 bytes from 10.0.2.1: icmp_seq=16 ttl=64 time=0.496 ms
The same thing will happen if I run in console:
# iwlist wlan0 scan

So the I think the problem is in NetworkManager or nm-applet are running
scan every two minutes, not in wpa_supplicant itself.

Ifound a workaround:
1. stop NetworkManager (/etc/init.d/network-manager stop)
2. write your wireless config for wpa_supplicant (my is simple I have open 
wireless network without password)
3. run wpa_supplicant (wpa_supplicant -iwlan0 -c 
/etc/wpa_supplicant/wpa_supplicant.conf)
4. get IP (dhclient3 wlan0)

I'm using ThinkPad X60 with
Ethernet controller: Atheros Communications Inc. AR5212 802.11abg NIC (rev 01)

-- 
wpa supplicant causes large timeouts
https://bugs.launchpad.net/bugs/460006
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