You might have a marginal power supply and/or a 7805 voltage regulator in the Vader that's starting to go bad. The Harmony Cart does draw more power than a standard 2K - 8K Atari cartridge.
I just spent too much time worrying about how the menu looked on the Harmony cart.The 7805 is new, I did a full tune-up on the console and replaced the caps and everything. I tried two different power supplies and had the same results. Both power supplies work fine on my Jr. and checked out OK with my meter. I'm thinking that the picture quality I have is normal and I was just expecting too much. Most of the time I've been playing on my 42 inch TV, which wasn't the best way to judge the picture quality. As long as I stick to a CRT with this 2600, the picture is fine. I just got hung up on the fact that the Harmony menu is clearer with my Jr. and my 7800. I'm thinking now that that wasn't a fair comparison. The only way I could do a real comparison would be with another revision 12 motherboard with the same mod. I'm not going to worry about it anymore. I'm just going to use this 2600 with my CRTs and use the Jr. and 7800 for my big LCDs.