The stock game has some issues, even with all the patching they did to it... Webster's GFO takes on a lot of those issues, and does seem to calm things down. Now, I have been attempting to see how much would be involved in moving the Narwhal Bonus Mod over into being compatible with Fall of the Rising Sun Ultimate (LOTS of issues!!!), and while doing so, I have found a couple of files out of place in the mod, though it looks like they're just duplicates, but I'll get back with you on that... in the meantime, there are a couple of threads around the site here about about getting the game to run its best for you.
Some of those are to have your Windows display set to the "native" resolution of your monitor. As an example, my old LCD here does 1280 x 1024 @ 70Hz as it's "native" resolution, which just means, that's what the LCD monitor is built for, and is most efficient at displaying. Therefore, I have my video card set to that resolution in Windows. I also have Silent Hunter set to that in the Options screen, Display settings off the main menu in the game. Also, once you're in the game, it's generally best not to <Alt> <Tab> out of the game. Some portions of the game on certain computers get "confused", such as the weather, sounds, and other things. While the game allows the use of 8096, try to stay away from anything over 2048, although that can make for a ~long~ session. TC (Time Compression) doesn't always cause trouble, but when it does, it's like the <Alt> <Tab>, in that it can be difficult to get re-set. Last but not least, when you go to Save your game, create a new save point, don't overwrite a previous save. Some of us just do like Patrol1Save2, Patrol1Save3, or whatever. Get to a certain point, and you "Delete" some of the old in-between saves.
A few last things about those "glitches" that you notice - when you're close to a base or close to a land mass, you'll see it. When an airplane is nearby, you'll see it. When a convoy is getting generated, or spawned, you'll see it, etc., so oftentimes, when you see the game "hiccup" like that, something is happening somewhere close-by in the game. Some folks use those little hiccups when they're in "enemy territory" to tell when something has spawned, and they'll quickly drop back to 1x TC and go to the sonar station to see if they can "hear" anything, then go hunt it down... my luck, I usually find a Hunter / Killer group...
Also, later in the game, there is a LOT going on, and a LOT for the game to keep track of, and that causes those hiccups.