I had the same problem and it took ages for me to understand what was going on. I thought I was doing somthing wrong but its a limitation of th software. This is taken from the readme which comes with the software. I think it will help if you have installed the 64 bit server using the client software.
64-BIT SUPPORT
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Managing 64-bit clients with the Symantec System Center
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To manage 64-bit clients with the Symantec System Center, configure the client settings so that the clients do not receive automatic virus definitions updates. The easiest way to configure the client settings is to configure a client group and place your 64-bit clients in this group. You can rely on users to click LiveUpdate, or you can set a LiveUpdate schedule for the group by using the Symantec System Center.
To manage 64-bit clients with the Symantec System Center:
1. Create a client group.
2. Right-click the client group.
3. Uncheck Inherit settings from Server Group.
4. Right-click the client group, and then select All Tasks > Symantec AntiVirus > Virus Definition Manager.
5. In the Virus Definition Manager dialog box, uncheck Update virus definitions from parent server.
6. Do one or both of the following:
- Uncheck Do not allow client to manually launch LiveUpdate.
- Check Schedule client for automatic updates using LiveUpdate, click Schedule, specify a schedule, and then click OK.
7. Click OK.
After you install 64-bit client software, drag the client computers into this client group.
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Side effects repair limitations
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64-bit antivirus clients support side effect repair only for 32-bit viruses and security risks that have infected the WOW64 portions of the 64-bit operating systems on AMD(R)/64 and EM64T hardware. 64-bit antivirus clients do not currently support the repair of 64-bit viruses and security risks on the 64-bit native operating system facilities outside of WOW64 on AMD/64 and EM64T hardware.