Are you using a third-party profile (E.G. from HCS Voice Packs), or have you created your own profile?
When you mention "use the Ships UI", are you executing any commands to do so? If so, have you checked to make sure all keypress actions are either set to "Press And Release Key(s)", or are matching pairs of "Press Key(s)" and "Release Key(s)"?
If you use a keypress action set to "Press Key(s)", due to the way Windows' keyboard system works, the key being pressed is assumed to remain pressed down until it is reported to be otherwise, either by software (like a keypress action set to "Release Key(s)"), or hardware (pressing and releasing the same key physically on your keyboard)
Stopping all commands, either through the button on VoiceAttack's main window, a keyboard key (combination) assigned to the "Stop All Commands Hotkey" option, or the "Make VoiceAttack Stop Processing All Commands" action in a command, will cause VoiceAttack to release any keys that are pressed down (including those on your physical keyboard, I.E. a message is sent to Windows to indicate that those keys are no longer pressed)
This can be used to try and confirm that the issue is a key being held down unintentionally by issuing the instruction to stop all commands when it occurs.