I compared this problem with two resolutions: 320x240 and 640x480 (both have the same aspect ratio, so the result is the same).
I used Visualboy Advance, playing Castlevania Aria of Sorrow, because (without stretch) you have a small and centered screen, with top and botton borders. Then, its easier to notice any change on the picture size. And also because a moon appears on the title screen (good to know if the aspect ratio is wrong or not).
As a video output, I used ArcadeVGA itself, Svideo output from ArcadeVGA and a Matrox Card running at 15khz through AdvanceCab (320x240 and 640x480).
The aspect ratio of the Svideo output and Matrox card was the same, but the ArcadeVGA picture was different from both. With Svideo and Matrox you can clearly see that the picture is much wider (which is correct, since we are talking about a GBA game) than the picture using ArcadeVGA (that looked like a square).
The moon from the game title screen, with the svideo and Matrox, is a perfect circle. But with ArcadeVGA it looks vertically stretched (or horizontally compressed)
I thought that playing GBA games with a 4:3 resolution really looked like this. And I always wondered why people didnt notice the wrong aspect ratio. But now I know the problem is with ArcadeVGA. Playing GBA with a PC Monitor and regular video card looks correct.
Is there any solution for this ? ArcadeVGA video modes are bad calibrated ?