Since you don't have much of a campaign file to worry too much about, I'd delete what is in the My Documents / SH4 folder, and start again. You are installed in a good folder, but if you're using a "short-cut" to start the game, is it pointed at the "GU.exe" file, or the "SH4.exe" file? Only use the "SH4.exe" file to start the game. Also, are you using "Run as administrator" on the file? What screen resolution are you trying to run the game at? What resolution is your computer set to?
The stock game does have some unrealistic groupings of ships, as you've already found, and some strange AI at times, so once you get things settled in, I'd go for some mods, like... oh, I don't know, maybe -
Fall of the Rising Sun Ultimate maybe?... or any of a number of other great choices...