Tom, I've never trusted the "scale bar" to give me an accurate sense of the true measurement of the map. For so long, this feature was screwed up with the stock game, I usually ignore it altogether. I took a second look at the map using a lower zoomed level and yes, the scale bar physical length actually stays the same in all zoomed screens. What changes is the listed measurement of the scale bar. It seems to be accurate. The image below is from the "Torpedo" training school mission.
In the above image the scale bar states the length is 3nm (nautical miles). When using the ruler, it measures 6050 yards. That's pretty close; actual conversion of 3nm to yards is 6076 yards. The ruler isn't going to give you a nuts-on measurement anyway, only in 50 yard increments. As the image shows, I've drawn a ruler line from the center of the sub out to the 3000 yard line. It still reads accurately.
I know if you change the graphic resolution on the game options page, you need to change the 3000 Yard Bearing Plotter to match the horizontal figure of the resolution you choose. That's why there are so many different versions of the Plotter. For example, changing the in-game resolution to 1024x768 you'll need to use the "3000 Yard Bearing Plotter (1024x)". The 4:3 aspect ratio is the same for both 1024x and the 1152x resolution. Unlike the OTC mod which has to match the aspect ratio of the game to have the periscope view corrected. To have the Plotter read correctly on the nav map you need to make a match with the horizontal resolution figure (not the aspect ratio).
Sorry I can't help you if you suspect the video card isn't up to snuff. As long as it's compatible to what SH4 states it should be, I'm at a loss to telling you any different.
I know the computer I've taken the images from isn't a cutting edge system; far from it. Over 8 years old! The video card is an AGP slot, ATI Radeon HD 4670, 1 GB of DDR3 ram. Hardly a power house now a days.
The mouse lag could be a clue to problems. That's not normal.