VoiceAttack's hotkeys work by hooking into Windows to receive key presses. If another application is also hooking into Windows or if a situation arises within Windows where VoiceAttack's hooks cannot receive those key presses, the hotkeys will cease to work. Going into the options screen will effectively reset the hooks - which means the hooks are working right up until something else is knocking them out (essentially, when it comes to hooking into Windows this way, the last man in wins). This is not a new issue, and it's not a VoiceAttack issue - it's just how Windows hooks work.
So, since the last man in wins, what you can do is just create a command in your profile that executes a, 'Windows Misc Function' action with the, 'Reset Keyboard Shortcuts' item selected. To do this, create a new command. Click, 'Other' then choose, 'Windows Misc Functions' then select, 'Reset Keyboard Shortcuts'. You can execute this command by voice next time your keyboard hook goes away.
On a side note, I'm looking at more ways to make VA's hooks more aggressive in terms of not being overridden. This would end up being a user preference for sure, as it may not be desirable for a lot of folks.