There can be side-effects with the use of PPIs - no drug is without side-effects unfortunately. They can include changes to bone density - more ease of fracture - and anemic states due to loss of B12 uptake.
Changes in bowel habits and loose stools can be a result of the use of PPIs. If you cut down on acid, you cut down on the amount of food that's thoroughly digested and able to be absorbed. Those materials will cause changes in the output of the digestive system in a number of ways.
I too have GERD, and I take the same medication as you. I have never had any problem with Prilosec, 20-mg. The OTC Prilosec is 10-mg, and I take two capsules a day if my prescription at the VA is late. I have never noticed my bowel movement smells any worst than it normally does. There is a test you can do to judge whether Prilosec is affecting your bowels. There are about 4 or 5 competitors to Prilosec. Examples are Zantac, Prevacid, 15-mg; Pepcid 20-mg. You can try one of these substitutes and determine whether one or two tablets takes care of your acid problem. All of these medications were one time prescription medicines, so the OTC strength may not be as strong as Prilosec. I keep both of the substitutes handy in case of an emergency.