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Does anyone have a Harmony flash cart for the Atari 2600? I have the standard one (not the Encore; I screwed up ordering and figure I won't worry about it until I find a game that I really want to play but can't), but I've had an odd issue with it and am still waiting for batari to message me back on AtariAge. The cart works perfectly with my 2600, but it won't work on my 7800. Both 7800 carts and retail 2600 carts play no problem on the 7800, but for some reason, the Harmony cart won't. I've tried updating the cartridge's firmware, but that didn't seem to help.

Any thoughts or ideas?

I have one, tho I never had a 5200 or 7800. I know that the Harmony cart will not work with a cart-modified Atari Flashback 2 (what I originally wanted to use it on), tho I think all original 2600 games will. I ended up buying a heavy sixer 2600 pre-modified for Composite and S-video for $75 on ebay years ago, and it's still going strong.
I don't know any more than that; it's too bad you cannot get it to work.

For what it's worth, the 7800 is very finicky. I'm 0 for 3 on perfectly working ones. They all looked clean but had their particular differing issues.

Al, AA owner, chimed in once on a troubleshooting thread of mine and agreed with above. He brings multiple to conventions bc they're so touchy, often after just working fine.

7800 emu is awesome so I finally just caved in.

The cart is worth more than your 7800 so hope it's the system