In my ISY portal/ connectivity tab/ Amazon Echo/ program/ my programs/ spoken mapping/ two programs are in red and the rest are black,  the ones in red won't let me do spoking mapping to them.

Anyone have any ideas why this is?

@Paulywog57 red usually means the program/device/etc is already in use. Black means it's available to be added to the Alexa skill.

Either change the number of items shown to 100 to see the full list (or at least 100 items if you have more than that - WOW!) or use the search box to look for a word in your program to find if it's already in use. You should be able to edit the line if already used in Alexa. Just remember to run "discovery" from the Alexa device (Alexa, discover devices) after you add a spoken. Also, make sure the spoken is unique and not already in use. 

And it looks like you can still use https://alexa.amazon.com/ (on a computer, NOT a mobile device!) just have to click on "Go to the previous version of alexa.amazon.com" and you can then click on "Smart Home"  (https://alexa.amazon.com/spa/index.html#smart-home) and then "Devices" to see what is currently in the Alexa skill all on one page.