Carlos,
This error is actually indicative of a registry flag in Windows 2003 that disables 16-bit applications from running on the system. When they are invoked, you get the error that you are seeing. For the record, I have NEVER run into this issue on a Unity server; however, most of my clients build with the default Cisco OS image but you can use a commercial image. In addition, group policy and such can be applied once servers are added to a domain so...I can't say where this stems from in your situation but it is what it is. There are 2 things I would look at.
1) All of the Unity Tools executables are stored in the Commserver folder. Just find one and it's individual executable file. See if you can run the executable in and of itself without the error.
2) HKLM\System\CurrentControlSet\Control\WOW\DisallowedPolicyDefault = 1, I believe this causes what you see. 0 would be disabled.
BEFORE YOU PROCEED - I do highly suggest you open a TAC case on this just to ensure that there isn't something else going on (e.g., potentially installation-related that needs resolution as well). In other words, I wouldn't go changing system registry keys unless you're completely comfortable with the system and ALWAYS backup the registry before you do anything. The other reason I say this is because I think this can be controlled at both a user and computer level and the computer level setting likely overrides user configurations. So, a quick chat with TAC would be best (you may need to ask to escalate beyond first level to get thru it more quickly).
HTH - if so, please rate.