You can rebuild the indexes but that probably won't help you. The indexes only allow you to search for the items it really has nothing to do with retrieval. The placeholders are just links to make HTTP calls to the server.
This may be unrelated but since you are using Windows 2003 SP1. You should always have these 2 reg keys set on your server. SP1 has issues if you refer to a server by an Alias name and I've seen issues with retrieval if these keys are not set.
Disable the loopback check
Follow these steps:1. Click Start, click Run, type regedit, and then click OK.
2. In Registry Editor, locate and then click the following registry key:
HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Lsa
3. Right-click Lsa, point to New, and then click DWORD Value.
4. Type DisableLoopbackCheck, and then press ENTER.
5. Right-click DisableLoopbackCheck, and then click Modify.
6. In the Value data box, type 1, and then click OK.
7. Quit Registry Editor, and then restart your computer.
2. Apply the following registry change to the file server. To do so, follow these steps: a. Start Registry Editor (Regedt32.exe).
b. Locate and click the following key in the registry:
HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\LanmanServer\Parameters
c. On the Edit menu, click Add Value, and then add the following registry value:
Value name: DisableStrictNameChecking
Data type: REG_DWORD
Radix: Decimal
Value: 1