David

Since you're new here, welcome. However, if you noticed, this forum only does PicBasicPro. You have here Microchip PIC-C18 code. It's not really the right place to post this. You could have posted it in 'off-topic' perhaps.

Having said that, I suppose, you're having a problem when the mux lines switch. That could be triggering the comparator interrupt. If you're using a PICKIT2, I think you can debug the problem easily enough.

I could suggest you
momentarily disable the comparators
do a mux select operation
clear comparator flags
enable the comparators

I'm not really sure if this will fix your issues, but it's worth a try.

Jerson