This editorial nicely explains how to analysis and manually organize the Boot.ini file in Microsoft Windows Server 2003.

You can rapidly and simply place the Boot.ini file to validate or correct the Microsoft Windows startup settings and do changes to the ARC (Advanced RISC Computing) path as required, in Windows Server 2003. In addition, you can include controls to the Boot.ini file.

Edit the Boot.ini file

Follow these steps to analysis and correct the Boot.ini file:
1. Click Start, point to Settings, and then click Control Panel.
2. In Control Panel, double-click System.
3. Click the Advanced tab, and then click Settings under Startup and Recovery.
4. Under System startup, click Edit.