I don't believe any of the issues are related to the Harmony.
#1 is due to the HMOVE bar, which is a side effect of repositioning objects (players, missile, ball) mid-screen for reuse. the Atari only has 2 players (sprites), 2 missiles, and a ball to move around, but can be reused multiple times going down the screen. Activision didn't like the sporadic black bars, so they forced them show up one very single scanline, which ends up making the image look like it's shifted to the right.
If the black bars show up on the black screen it just means you have your display set too bright or with too much contrast. That's because the black of the HMOVE bar is not the same as color black.
Screenshots from Stella:
#2 possibly a bad ROM file. Or perhaps you're not playing it correctly - for Decathlon you need to rapidly move the joystick left/right to make the man run. You can reference most of the manuals from the main page of AtariAge. At the bottom of the left side menu is a Title Search. Search for "decath" and you'll be able to get to the manual.
#3 one issue with the 2600 is the games, not the console, dictate how many scanlines are drawn. Some displays have trouble if they don't receive exactly 262 scanlines for NTSC based games (312 for PAL). Digital Press created a scanline list a while back that shows how much discrepancy there is between games - some NTSC games output as few as 237 or as many as 290! I suspect your VGA monitor doesn't like the signal put out by your Atari.