Same problem here too on a macbook pro 2.1. Disconnections every 2 minutes and I have to wait 2 minutes again to regain connection. The link is of very poor quality : less than 3mbit/s. (can't even watch my ISP's tv streaming service)
Now I'm connected manually via iwconfig. No disconnections and good speed so it's not a driver problem (ath9k).

Using jaunty alpha6 fresh install and up to date. Network-manager 0.7.1~rc3.1.git4cf2da146-0ubuntu1

$ cat /etc/network/interfaces 
auto lo
iface lo inet loopback

$ uname -a
Linux mbpc2d 2.6.28-11-generic #37-Ubuntu SMP Mon Mar 23 16:40:00 UTC 2009 x86_64 GNU/Linux

$ lspci -vvnn
...
00:1e.0 PCI bridge [0604]: Intel Corporation 82801 Mobile PCI Bridge [8086:2448] (rev e2) (prog-if 01)
	Control: I/O+ Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
	Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=fast >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
	Latency: 0
	Bus: primary=00, secondary=0c, subordinate=0c, sec-latency=32
	Memory behind bridge: 94000000-940fffff
	Secondary status: 66MHz- FastB2B+ ParErr- DEVSEL=medium >TAbort- <TAbort- <MAbort+ <SERR- <PERR-
	BridgeCtl: Parity- SERR- NoISA- VGA- MAbort- >Reset- FastB2B-
		PriDiscTmr- SecDiscTmr- DiscTmrStat- DiscTmrSERREn-
	Capabilities: [50] Subsystem: Gammagraphx, Inc. (or missing ID) Device [0000:0000]
...

03:00.0 Network controller [0280]: Atheros Communications Inc. AR5008 Wireless Network Adapter [168c:0024] (rev 01)
	Control: I/O+ Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
	Status: Cap+ 66MHz- UDF- FastB2B- ParErr- DEVSEL=fast >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
	Latency: 0, Cache Line Size: 256 bytes
	Interrupt: pin A routed to IRQ 17
	Region 0: Memory at 98100000 (64-bit, non-prefetchable) [size=64K]
	Capabilities: [40] Power Management version 2
		Flags: PMEClk- DSI- D1+ D2- AuxCurrent=375mA PME(D0+,D1+,D2-,D3hot+,D3cold-)
		Status: D0 PME-Enable- DSel=0 DScale=0 PME-
	Capabilities: [50] Message Signalled Interrupts: Mask- 64bit- Queue=0/0 Enable-
		Address: 00000000  Data: 0000
	Capabilities: [60] Express (v1) Legacy Endpoint, MSI 00
		DevCap:	MaxPayload 128 bytes, PhantFunc 0, Latency L0s <128ns, L1 <2us
			ExtTag- AttnBtn- AttnInd- PwrInd- RBE- FLReset-
		DevCtl:	Report errors: Correctable- Non-Fatal- Fatal- Unsupported-
			RlxdOrd+ ExtTag- PhantFunc- AuxPwr- NoSnoop-
			MaxPayload 128 bytes, MaxReadReq 512 bytes
		DevSta:	CorrErr- UncorrErr+ FatalErr- UnsuppReq+ AuxPwr- TransPend-
		LnkCap:	Port #0, Speed 2.5GT/s, Width x1, ASPM L0s L1, Latency L0 <512ns, L1 <64us
			ClockPM- Suprise- LLActRep- BwNot-
		LnkCtl:	ASPM L1 Enabled; RCB 128 bytes Disabled- Retrain- CommClk+
			ExtSynch- ClockPM- AutWidDis- BWInt- AutBWInt-
		LnkSta:	Speed 2.5GT/s, Width x1, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
	Capabilities: [90] MSI-X: Enable- Mask- TabSize=1
		Vector table: BAR=0 offset=00000000
		PBA: BAR=0 offset=00000000
	Capabilities: [100] Advanced Error Reporting <?>
	Capabilities: [140] Virtual Channel <?>
	Kernel driver in use: ath9k
	Kernel modules: ath9k

syslog extract : 

Mar 26 00:09:26 mbpc2d NetworkManager: <debug> [1238022566.001643] periodic_update(): Roamed from BSSID 12:34:56:78:90:ab (crepe_au_sucre) to (none) ((none)) 
Mar 26 00:09:32 mbpc2d NetworkManager: <debug> [1238022572.000653] periodic_update(): Roamed from BSSID (none) ((none)) to 12:34:56:78:90:ab (crepe_au_sucre) 
Mar 26 00:12:26 mbpc2d NetworkManager: <debug> [1238022746.001589] periodic_update(): Roamed from BSSID 12:34:56:78:90:ab (crepe_au_sucre) to (none) ((none)) 
Mar 26 00:12:32 mbpc2d NetworkManager: <debug> [1238022752.000758] periodic_update(): Roamed from BSSID (none) ((none)) to 12:34:56:78:90:ab (crepe_au_sucre) 
Mar 26 00:14:26 mbpc2d NetworkManager: <debug> [1238022866.001591] periodic_update(): Roamed from BSSID 12:34:56:78:90:ab (crepe_au_sucre) to (none) ((none)) 
Mar 26 00:14:32 mbpc2d NetworkManager: <debug> [1238022872.000197] periodic_update(): Roamed from BSSID (none) ((none)) to 12:34:56:78:90:ab (crepe_au_sucre) 
Mar 26 00:16:26 mbpc2d NetworkManager: <debug> [1238022986.001536] periodic_update(): Roamed from BSSID 12:34:56:78:90:ab (crepe_au_sucre) to (none) ((none)) 
Mar 26 00:16:32 mbpc2d NetworkManager: <debug> [1238022992.000291] periodic_update(): Roamed from BSSID (none) ((none)) to 12:34:56:78:90:ab (crepe_au_sucre) 
Mar 26 00:18:26 mbpc2d NetworkManager: <debug> [1238023106.001596] periodic_update(): Roamed from BSSID 12:34:56:78:90:ab (crepe_au_sucre) to (none) ((none)) 
Mar 26 00:18:32 mbpc2d NetworkManager: <debug> [1238023112.000182] periodic_update(): Roamed from BSSID (none) ((none)) to 12:34:56:78:90:ab (crepe_au_sucre) 
....

The complete syslog file is attached and contains association errors at the beginning because I changed my AP security from WPA PSK to WEP (just in case).