Thanks, menu is file > document color mode and is set to RGB.
The AI file you posted is CMYK:
I think the problem is that all interactive PDFs have their color converted into sRGB, and because you have a mix of color spaces and missing profiles the conversion to sRGB on export is variable.
Converting the AI file to sRGB should solve the problem—I would save a copy of the original.
Make sure you Illustrator Color Settings' RGB Working space is sRGB:
Set the AI Document Color Mode to RGB, which will convert all color to sRGB.
Resave the file and check Embed ICC Profiles
Update or relink to the RGB file in ID and make sure ID's RGB Working Space is also sRGB, then try the export.
I can't really test here without your problem ID files, but if the above doesn't work post them.