Once you get a thermometer and know what your temps are, the next thing you need to look at is what's changing colors: Plastic, Glitter, Colorant. To do this you will need to break it down and just make clear baits, then try making clear baits with your glitter, then try it with just colorant, then with all three. There are only 4 variables you are dealing with: heat, plastic, colorant and glitter. It's just a process of determining which is causing the problem and then it will be easier to suggest a solution.
Shorter cycles and lower heat may be the answer, but adding your glitter at a different point of the process may be the answer. It would also be very helpful if you could share the brands of products you are using and the environment you are working in (i.e. 1000 Watt microwave with or without turntable - 5 years old).
Going through this process now will save you a lot of time, money and frustration over the long run.
Jason