What can I use as a thickening agent in my homemade hair conditioner?

Try plain gelatin. It is actually found in many conditioners and it will also boost the strength of your hair. Don't put in too much, or your conditioner will be solid.

what do you have in your home made conditioner it could be that some of the ingredients are reacting against each other

if i could have the ingredient you have made up i will be able to tell you a solution

You could try whipped egg whites. Eggs help the hair shine

will these things reacting?