You probably haven't told your Windows PC what part of the world you're in. Without that information it can't offset the "Internet time" to the correct value.

• Right-click the clock in the bottom right-hand corner
• Choose the menu option "Adjust date/time"
• Click the button [Change time zone...]
• Choose the correct capital city of other significant town for the region that you are in
• If your region uses Daylight Saving Time (i.e. the time changes by an hour twice a year), tick that box too

Since your PC is being told its clock is 9 hours behind, likely candidates for your local region are Tokyo, Seoul or Yakutsk. Alternatively, if I've misunderstood your explanation of which way the clock is wrong, you might be in Alaska.

Based our investigations it seems that your Amsterdam entry in the timezone database may be corrupted. This article from the Microsoft Technet gives a little explanation of the Timezone database in the registry. Looking at HKLM\SOFTWARE\Microsoft\Windows NT\CurrentVersion\Time Zones I can find an entry for W. Europe Standard Time that corresponds to the Amsterdam timezone. Here are entries from a Windows 7 PC that appear to work correctly:

Display     REG_SZ     (UTC+01:00) Amsterdam, Berlin, Bern, Rome, Stockholm, Vienna
Dlt         REG_SZ     W. Europe Daylight Time
MUI_Display REG_SZ     @tzred.dll,-320
MUI_Dlt     REG_SZ     @tzres.dll,-321
MUI_Std     REG_SZ     @tzres.dll,-322
Std         REG_SZ     W. Europe Standard Time
TZI         REG_BINARY C4 FF FF FF 00 00 00 00 C4 FF FF FF 00 00 0A 00 00 00 05 00 03 00 00 00 00 00 00 00 00 00 03 00 00 00 05 00 02 00 00 00 00 00 00 00

I would highly suspect Ubuntu and Windows disagreeing on whether the hwclock is localtime or UTC. The conflict usually comes about because Linux uses the the hwclock set in UTC, while Windows uses the hwclock set to the localtime zone.

If you want your hwclock to show the time in your timezone, then you will need to change linux to not be UTC, which means make linux use localtime. If you are OK with your hwclock (BIOS) to be in UTC, then change windows to be UTC.

From here:

Make Windows use UTC

Note: This method was not initially supported on Windows Vista and Server 2008, but came back with Vista SP2, Windows 7, Server 2008 R2 and Windows 8/8.1.

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To make MS Windows calculate the time from the hardware clock as UTC.

Create a file named WindowsTimeFixUTC.reg with the following contents and then double click on it to merge the contents with the registry:

Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\TimeZoneInformation]
 "RealTimeIsUniversal"=dword:00000001

Note: Windows Time service will still write local time to the RTC regardless of the registry setting above on shutdown, so it is handy to disable Windows Time service with this command (if time sync is still required while in Windows use any third-party time sync solution):

sc config w32time start= disabled

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Reversing the change.

You can create a file with the following contents and then double-click it to merge in the original changes, as above:

Windows Registry Editor Version 5.00

[HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\TimeZoneInformation]
    "RealTimeIsUniversal"=-

If Windows Time service was disabled, enable it again with the command:

sc config w32time start= demand

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Make Linux use 'Local' time

To tell your Ubuntu system that the hardware clock is set to 'local' time:

Pre-Ubuntu 15.04 systems (e.g. Ubuntu 14.04 LTS):

edit /etc/default/rcS and add or change the following section

#Set UTC=yes if your hardware clock is set to UTC (GMT)
UTC=no

Ubuntu 15.04 systems and above (e.g. Ubuntu 16.04 LTS): open a terminal and execute the following command:

timedatectl set-local-rtc 1