I have have this problem too. I have a Acer 5737z Nootebook. It only works with a card at boot (Jaunty).


05:00.0 System peripheral: JMicron Technologies, Inc. SD/MMC Host Controller
	Subsystem: Acer Incorporated [ALI] Device 0160
	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: 64 bytes
	Interrupt: pin A routed to IRQ 23
	Region 0: Memory at f0500000 (32-bit, non-prefetchable) [size=256]
	Capabilities: [a4] Power Management version 3
		Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
		Status: D0 PME-Enable- DSel=0 DScale=0 PME-
	Capabilities: [80] Express (v1) Endpoint, MSI 00
		DevCap:	MaxPayload 128 bytes, PhantFunc 0, Latency L0s <64ns, L1 <1us
			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 #1, Speed 2.5GT/s, Width x1, ASPM L0s L1, Latency L0 unlimited, L1 unlimited
			ClockPM- Suprise- LLActRep- BwNot-
		LnkCtl:	ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk+
			ExtSynch- ClockPM- AutWidDis- BWInt- AutBWInt-
		LnkSta:	Speed 2.5GT/s, Width x1, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
	Capabilities: [94] Message Signalled Interrupts: Mask- 64bit- Queue=0/0 Enable-
		Address: fffffffc  Data: 0000
	Kernel driver in use: sdhci-pci
	Kernel modules: sdhci-pci

05:00.2 SD Host controller: JMicron Technologies, Inc. Standard SD Host Controller (prog-if 01)
	Subsystem: Acer Incorporated [ALI] Device 0160
	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-
	Interrupt: pin A routed to IRQ 23
	Region 0: Memory at f0500400 (32-bit, non-prefetchable) [size=256]
	Capabilities: [a4] Power Management version 3
		Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
		Status: D0 PME-Enable- DSel=0 DScale=0 PME-
	Capabilities: [80] Express (v1) Endpoint, MSI 00
		DevCap:	MaxPayload 128 bytes, PhantFunc 0, Latency L0s <64ns, L1 <1us
			ExtTag- AttnBtn- AttnInd- PwrInd- RBE+ FLReset-
		DevCtl:	Report errors: Correctable- Non-Fatal- Fatal- Unsupported-
			RlxdOrd+ ExtTag- PhantFunc- AuxPwr- NoSnoop-
			MaxPayload 128 bytes, MaxReadReq 128 bytes
		DevSta:	CorrErr- UncorrErr- FatalErr- UnsuppReq+ AuxPwr- TransPend-
		LnkCap:	Port #1, Speed 2.5GT/s, Width x1, ASPM L0s L1, Latency L0 unlimited, L1 unlimited
			ClockPM- Suprise- LLActRep- BwNot-
		LnkCtl:	ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk+
			ExtSynch- ClockPM- AutWidDis- BWInt- AutBWInt-
		LnkSta:	Speed 2.5GT/s, Width x1, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
	Capabilities: [94] Message Signalled Interrupts: Mask- 64bit- Queue=0/0 Enable-
		Address: fffffffc  Data: 0000
	Kernel modules: sdhci-pci

05:00.3 System peripheral: JMicron Technologies, Inc. MS Host Controller
	Subsystem: Acer Incorporated [ALI] Device 0160
	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: 64 bytes
	Interrupt: pin A routed to IRQ 11
	Region 0: Memory at f0500800 (32-bit, non-prefetchable) [size=256]
	Capabilities: [a4] Power Management version 3
		Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
		Status: D0 PME-Enable- DSel=0 DScale=0 PME-
	Capabilities: [80] Express (v1) Endpoint, MSI 00
		DevCap:	MaxPayload 128 bytes, PhantFunc 0, Latency L0s <64ns, L1 <1us
			ExtTag- AttnBtn- AttnInd- PwrInd- RBE+ FLReset-
		DevCtl:	Report errors: Correctable- Non-Fatal- Fatal- Unsupported-
			RlxdOrd+ ExtTag- PhantFunc- AuxPwr- NoSnoop-
			MaxPayload 128 bytes, MaxReadReq 128 bytes
		DevSta:	CorrErr- UncorrErr- FatalErr- UnsuppReq+ AuxPwr- TransPend-
		LnkCap:	Port #1, Speed 2.5GT/s, Width x1, ASPM L0s L1, Latency L0 unlimited, L1 unlimited
			ClockPM- Suprise- LLActRep- BwNot-
		LnkCtl:	ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk+
			ExtSynch- ClockPM- AutWidDis- BWInt- AutBWInt-
		LnkSta:	Speed 2.5GT/s, Width x1, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
	Capabilities: [94] Message Signalled Interrupts: Mask- 64bit- Queue=0/0 Enable-
		Address: fffffffc  Data: 0000

05:00.4 System peripheral: JMicron Technologies, Inc. xD Host Controller
	Subsystem: Acer Incorporated [ALI] Device 0160
	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: 64 bytes
	Interrupt: pin A routed to IRQ 11
	Region 0: Memory at f0500c00 (32-bit, non-prefetchable) [size=256]
	Capabilities: [a4] Power Management version 3
		Flags: PMEClk- DSI- D1- D2- AuxCurrent=0mA PME(D0-,D1-,D2-,D3hot-,D3cold-)
		Status: D0 PME-Enable- DSel=0 DScale=0 PME-
	Capabilities: [80] Express (v1) Endpoint, MSI 00
		DevCap:	MaxPayload 128 bytes, PhantFunc 0, Latency L0s <64ns, L1 <1us
			ExtTag- AttnBtn- AttnInd- PwrInd- RBE+ FLReset-
		DevCtl:	Report errors: Correctable- Non-Fatal- Fatal- Unsupported-
			RlxdOrd+ ExtTag- PhantFunc- AuxPwr- NoSnoop-
			MaxPayload 128 bytes, MaxReadReq 128 bytes
		DevSta:	CorrErr- UncorrErr- FatalErr- UnsuppReq+ AuxPwr- TransPend-
		LnkCap:	Port #1, Speed 2.5GT/s, Width x1, ASPM L0s L1, Latency L0 unlimited, L1 unlimited
			ClockPM- Suprise- LLActRep- BwNot-
		LnkCtl:	ASPM Disabled; RCB 64 bytes Disabled- Retrain- CommClk+
			ExtSynch- ClockPM- AutWidDis- BWInt- AutBWInt-
		LnkSta:	Speed 2.5GT/s, Width x1, TrErr- Train- SlotClk+ DLActive- BWMgmt- ABWMgmt-
	Capabilities: [94] Message Signalled Interrupts: Mask- 64bit- Queue=0/0 Enable-
		Address: fffffffc  Data: 0000

Apr 25 19:19:13 Notebook kernel: [   11.746008] sdhci: Secure Digital Host Controller Interface driver
Apr 25 19:19:13 Notebook kernel: [   11.746011] sdhci: Copyright(c) Pierre Ossman
Apr 25 19:19:13 Notebook kernel: [   11.817898] sdhci-pci 0000:05:00.0: SDHCI controller found [197b:2382] (rev 0)
Apr 25 19:19:13 Notebook kernel: [   11.817927] sdhci-pci 0000:05:00.0: PCI INT A -> Link[Z011] -> GSI 23 (level, low) -> IRQ 23
Apr 25 19:19:13 Notebook kernel: [   11.817997] sdhci-pci 0000:05:00.0: setting latency timer to 64
Apr 25 19:19:13 Notebook kernel: [   11.818053] mmc0: SDHCI controller on PCI [0000:05:00.0] using ADMA
Apr 25 19:19:13 Notebook kernel: [   11.818064] sdhci-pci 0000:05:00.2: SDHCI controller found [197b:2381] (rev 0)
Apr 25 19:19:13 Notebook kernel: [   11.818079] sdhci-pci 0000:05:00.2: PCI INT A -> Link[Z011] -> GSI 23 (level, low) -> IRQ 23
Apr 25 19:19:13 Notebook kernel: [   11.818086] sdhci-pci 0000:05:00.2: Refusing to bind to secondary interface.
Apr 25 19:19:13 Notebook kernel: [   11.818092] sdhci-pci 0000:05:00.2: PCI INT A disabled