Well I may have spoken too soon
It appears I may have a corrosion issue on the input connector. I've sprayed out the connector with contact cleaner. I've tried two cables and they both act different. I'll try to get a 3rd and 4th tomorrow.
The original cable will disable channels 2,4, 6, and 7. The radio shack cable allows 1,3,5,7,8 to function normally and channels 2,4,6 to function as described below.
Independently they will not function however... if you activate one of those channels (2,4, or 6) it will allow one of the remaining channels to function but not both. So... you can activate channel 2, it will not work. If you then activate channel 4, it will work. If you then activate channel 6 it will not work. If you activate channel 2, then 4, then 6, channels 2 and 6 will not function.... You can do it in any order with those 3 channels but the results are still the same. The second in the sequence is the only one to function.
Any ideas? I'm thinking the connector on the relay box has corroded and needs replacing.