Same problem here with hardy, alcor and nforce430.

2.6.24-24-generic #1 SMP Wed Apr 15 15:11:35 UTC 2009 x86_64 GNU/Linux

$ lspci|grep -i usb
00:02.0 USB Controller: nVidia Corporation MCP61 USB Controller (rev a3)
00:02.1 USB Controller: nVidia Corporation MCP61 USB Controller (rev a3)

$ lsusb
Bus 002 Device 002: ID 051d:0002 American Power Conversion Uninterruptible Power Supply
Bus 002 Device 001: ID 0000:0000
Bus 001 Device 012: ID 058f:6362 Alcor Micro Corp. Hi-Speed 21-in-1 Flash Card Reader/Writer (Internal/External)
Bus 001 Device 001: ID 0000:0000

# grep -i usb <dmesg
[   93.997664] usbcore: registered new interface driver usbfs
[   93.997691] usbcore: registered new interface driver hub
[   93.997725] usbcore: registered new device driver usb
[   94.000699] ehci_hcd 0000:00:02.1: new USB bus registered, assigned bus number 1
[   94.003812] ohci_hcd: 2006 August 04 USB 1.1 'Open' Host Controller (OHCI) Driver
[   94.014663] ehci_hcd 0000:00:02.1: USB 2.0 started, EHCI 1.00, driver 10 Dec 2004
[   94.014807] usb usb1: configuration #1 chosen from 1 choice
[   94.014834] hub 1-0:1.0: USB hub found
[   94.119479] ohci_hcd 0000:00:02.0: new USB bus registered, assigned bus number 2
[   94.178035] usb usb2: configuration #1 chosen from 1 choice
[   94.178067] hub 2-0:1.0: USB hub found
[   94.574386] usb 1-9: new high speed USB device using ehci_hcd and address 3
[   94.704594] usb 1-9: configuration #1 chosen from 1 choice
[   95.005899] usb 2-3: new low speed USB device using ohci_hcd and address 2
[   95.230333] usb 2-3: configuration #1 chosen from 1 choice
[   95.237653] usbcore: registered new interface driver libusual
[   95.242915] Initializing USB Mass Storage driver...
[   95.243006] scsi2 : SCSI emulation for USB Mass Storage devices
[   95.243082] usbcore: registered new interface driver usb-storage
[   95.243086] USB Mass Storage support registered.
[   95.243253] usb-storage: device found at 3
[   95.243256] usb-storage: waiting for device to settle before scanning
[   95.249629] usbcore: registered new interface driver hiddev
[   96.669636] hiddev96hidraw0: USB HID v1.10 Device [American Power Conversion Smart-UPS 1000 FW:652.18.I USB FW:7.3] on usb-0000:00:02.0-3
[   96.669657] usbcore: registered new interface driver usbhid
[   96.669662] /build/buildd/linux-2.6.24/drivers/hid/usbhid/hid-core.c: v2.6:USB HID core driver
[  100.238536] usb-storage: device scan complete
[  100.239143] scsi 2:0:0:0: Direct-Access     Generic  USB SD Reader    1.00 PQ: 0 ANSI: 0
[  100.239635] scsi 2:0:0:1: Direct-Access     Generic  USB CF Reader    1.01 PQ: 0 ANSI: 0
[  100.240134] scsi 2:0:0:2: Direct-Access     Generic  USB SM Reader    1.02 PQ: 0 ANSI: 0
[  100.240632] scsi 2:0:0:3: Direct-Access     Generic  USB MS Reader    1.03 PQ: 0 ANSI: 0

and then the fun starts (no usb activity on bus 1 at this time)

Jun 13 12:07:23 server kernel: [523139.052749] usb 1-9: reset high speed USB device using ehci_hcd and address 12
Jun 13 12:09:27 server kernel: [523206.095530] usb 1-9: reset high speed USB device using ehci_hcd and address 12
Jun 13 12:10:18 server kernel: [523228.260320] usb 1-9: reset high speed USB device using ehci_hcd and address 12
Jun 13 12:13:18 server kernel: [523306.481562] usb 1-9: reset high speed USB device using ehci_hcd and address 12

USB2.0 port on the card reader in question works fine though with various flash sticks and a camera.