Nope, the manual is correct:
03:00.0 PCI bridge: Intel Corporation 82801 PCI Bridge (rev 41) (prog-if 01 [Subtractive decode])
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
Bus: primary=03, secondary=04, subordinate=04, sec-latency=32
I/O behind bridge: 0000c000-0000cfff
Memory behind bridge: d0a00000-d0bfffff
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: [90] Power Management version 2
Flags: PMEClk- DSI- D1+ D2+ AuxCurrent=55mA PME(D0+,D1+,D2+,D3hot+,D3cold+)
Status: D0 NoSoftRst- PME-Enable- DSel=0 DScale=0 PME-
Capabilities: [a0] Subsystem: Gigabyte Technology Co., Ltd Device 8892
04:00.0 Ethernet controller: Intel Corporation 82546GB Gigabit Ethernet Controller (rev 03)
Subsystem: Intel Corporation PRO/1000 MT Dual Port Server Adapter
Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
Status: Cap+ 66MHz+ UDF- FastB2B- ParErr- DEVSEL=medium >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 64 (63750ns min), Cache Line Size: 64 bytes
Interrupt: pin A routed to IRQ 18
Region 0: Memory at d0b20000 (64-bit, non-prefetchable) [size=128K]
Region 2: Memory at d0ac0000 (64-bit, non-prefetchable) [size=256K]
Region 4: I/O ports at c040 [disabled] [size=64]
Expansion ROM at d0a80000 [disabled] [size=256K]
Capabilities: [dc] Power Management version 2
Flags: PMEClk- DSI+ D1- D2- AuxCurrent=0mA PME(D0+,D1-,D2-,D3hot+,D3cold+)
Status: D0 NoSoftRst- PME-Enable- DSel=0 DScale=1 PME-
Capabilities: [e4] PCI-X non-bridge device
Command: DPERE- ERO+ RBC=512 OST=1
Status: Dev=00:00.0 64bit+ 133MHz+ SCD- USC- DC=simple DMMRBC=2048 DMOST=1 DMCRS=16 RSCEM- 266MHz- 533MHz-
Kernel driver in use: e1000
04:00.1 Ethernet controller: Intel Corporation 82546GB Gigabit Ethernet Controller (rev 03)
Subsystem: Intel Corporation PRO/1000 MT Dual Port Server Adapter
Control: I/O- Mem+ BusMaster+ SpecCycle- MemWINV- VGASnoop- ParErr- Stepping- SERR- FastB2B- DisINTx-
Status: Cap+ 66MHz+ UDF- FastB2B- ParErr- DEVSEL=medium >TAbort- <TAbort- <MAbort- >SERR- <PERR- INTx-
Latency: 64 (63750ns min), Cache Line Size: 64 bytes
Interrupt: pin B routed to IRQ 19
Region 0: Memory at d0b00000 (64-bit, non-prefetchable) [size=128K]
Region 2: Memory at d0a40000 (64-bit, non-prefetchable) [size=256K]
Region 4: I/O ports at c000 [disabled] [size=64]
Expansion ROM at d0a00000 [disabled] [size=256K]
Capabilities: [dc] Power Management version 2
Flags: PMEClk- DSI+ D1- D2- AuxCurrent=0mA PME(D0+,D1-,D2-,D3hot+,D3cold+)
Status: D0 NoSoftRst- PME-Enable- DSel=0 DScale=1 PME-
Capabilities: [e4] PCI-X non-bridge device
Command: DPERE- ERO+ RBC=512 OST=1
Status: Dev=00:00.1 64bit+ 133MHz+ SCD- USC- DC=simple DMMRBC=2048 DMOST=1 DMCRS=16 RSCEM- 266MHz- 533MHz-
Kernel driver in use: e1000
As you can see, the bridge supports 66MHz operation, but has been locked to 33MHz. No sure why the PCI-X card is reporting 66MHz+ instead of 66MHz- in its status via lspci. Checking dmesg suggests it is operating at 33MHz.
The support from Gigabyte reps here is almost as poor as the BIOS on this board. It often reports 'BIOS corruption' and reflashes from the secondary chip on reboot. Thermald doesn't work correctly because the DTS implementation is bad. ASPM also doesn't work, but I think that is a firmware issue.
I'd recommend linux users stay away from this board; even the F3 BIOS is a hacky mess.