If you eating alot of of pre-packaged GF foods, then yes, the guar and xanthum gum found in large amounts in these products can cause cramping and loose stools, especially if your body isn't used to them. Not to mention the tons of sugar and fat they throw in there to try and make it taste better.
There's nothing wrong with guar and xanthum, they replace the chewy-elasticity gluten provided, you just need to go easy on them till your body adjusts. Baking mixes tend to have less guar/xanthum than packaged foods, try a pancake mix (Pamela's, Kinnikinnick's). Bob's Red Mill sells pure rice flour, rice flour sugar cookies are fairly simple to make - and no "gum".
Mixed with corn flour, the pancake mixes make great corn muffins too.
GF since '05