I confirm this on Mainboard Gigabyte GA-P35-DS4 with r8169.
After resume from S3 speed is 100Mbit/s.

r...@k1:/home/kede#  ethtool eth0
Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
        Advertised auto-negotiation: Yes
        Speed: 100Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: g
        Current message level: 0x00000033 (51)
        Link detected: yes


The following command brings back 1000Mbit:
r...@k1:/home/kersten# ethtool -s eth0 speed 1000

The onboard LEDs and the switch indicate 1000 Mbit now.
The network-manager-applet from gnome however still shows 100mbit.


r...@k1:/home/kersten# ethtool eth0
Settings for eth0:
        Supported ports: [ TP MII ]
        Supported link modes:   10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Supports auto-negotiation: Yes
        Advertised link modes:  10baseT/Half 10baseT/Full 
                                100baseT/Half 100baseT/Full 
                                1000baseT/Half 1000baseT/Full 
        Advertised auto-negotiation: Yes
        Speed: 1000Mb/s
        Duplex: Full
        Port: MII
        PHYAD: 0
        Transceiver: internal
        Auto-negotiation: on
        Supports Wake-on: pumbg
        Wake-on: g
        Current message level: 0x00000033 (51)
        Link detected: yes

-- 
Realtek RTL8111/8169 LAN (r8169) falls back from Gigabit to 100Mb/s after 
waking up from Suspend(S3)
https://bugs.launchpad.net/bugs/331699
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