Well, I've had this happen to me more than a few occasions now. This is where the console appears to remain minimized. Doesn't seem to affect functionality but can get really annoying. I'm not sure what exactly causes it but I'm going to post the fix here so I don't have to look for it every time happens.
Virutal PC has an aptly named file called options.xml to maintain settings related to the console. Its located here:
C:\Documents and Settings\{windows account name}\Application
Data\Microsoft\Virtual PC\Options.xml
(Replace {windows account name} with your windows account name)
What we're interested is in this set of tags:
<window>
<console>
{...snip...}
<left_position type="integer">0</left_position>
<top_position type="integer">0</top_position>
{...snip...}
</console>
{...snip...}
</window>
You should have some obscene values for the above keys. Just reset them to 0, restart Virtual PC and you're good to go.