Simple syrup crystalizes

Carolblymire didn't have her "On Food and Cooking" handy but I have mine right here. The issue is that as the syrup cools, the molecules tighten up and precipitate the crystals. The amount of precipitate depends on the solution, temperature, humidity (it can reabsorb water in humid temperatures), and how rapidly it cools down. I agree that you might want to find a copy at your library or bookstore and see if you can forensically figure out how your set of circumstances are producing this result. McGee includes photos of crystals that can help you figure it out.

Another option is to make simple syrup without heat involved. Similar process: put equal amounts water and sugar in the container, shake, wait for 5 minutes, shake again, then let it sit until clear. I don't know if storage will result in crystallization (my chemistry knowledge is lacking), but if as carolblymire says the heating and cooling process plays a part, this would at least take that out of the equation.

what is your sugar water ratio. Sounds to me like you have a saturated solution and over time it breaks down much easier. I am guessing if you add water to it would take care of the problem. I know with honey it has to do with the particulates and the amount of moisture retained in the honey.

You could add some glucose or fructose (such as corn syrup or agave) to help interfere with the sucrose's ability to form a crystalline matrix. You could also add a little lemon juice or cream of tartar to 'invert' some of the sucrose molecules (breaks the sucrose into fructose and glucose molecules.) Or just make fresh more often.

The sugar molecules got too crowded when they dissolved, and the water molecules couldn't separate them. Thus, the sugar molecules bonded together into a crystal formation. The temperature to which you heated it, and then the rate it which it cools all play into this happening. When it's processed, cane sugar is heated less than other sugars, so when you make simple syrup with it -- if I'm remembering correctly -- you need to really be careful that you're doing a 1:1 ratio, and bring it up to a simmer gently, and let it simmer for about a minute before turning off the burner. Then, let it cool to room temp naturally. McGee's "On Food and Cooking" has a great section about sugars, and the chemistry of what they do at different heats. Probably best to consult that to be 100% accurate (I'm not near my copy of it right now, or I'd look it up for ya.)

A simple syrup involves inexpensive ingredients: sugar and water. It's better to make it as needed rather than bottle and hold it.

That's chemistry! Making sure that your container is very clean can help. Also adding a little bit of corn syrup.