I ha dthe EXACT same issue with my Niveus Media Center with Windows Vista, i.e. that the commands only worked the first time and not the second time unless another command was sent in between. The following solved it:

Change Registry key
HKEY_LOCAL_MACHINE\SYSTEM\ControlSet001\Services\HidIr\Remotes\745a17a0-74d3-11d0-b6fe-00a0c90f57da
from "1" to "0" and reboot the system.

MANY thanks for finding this out as Universal Remote tech support didn't seem to know about this.

Hawk