I feel that despite it not being refigerated, that there is still billions of the culture for it to work. At the most it probably loses a few billion of the count, but it still has a high count overall.
The IBS is normal because that means the probiotic is working; the IBS is caused by the dead candida flooding your gut. Like you said, the best way to reduce this is to stop taking the probiotic for a few days and then start again. You may have started at a too high of a count also; consider going for a 20-30 billion count and then working up to the 50 or 80 billion count.
The probiotic is one of the keys to recovery from candida; it may be the most important thing to help you recover other than drinking plenty of water, getting plenty of rest, and the proper diet.
Another probiotic to consider taking is the HMF neuro; this contains human micro flora which binds better to the intestine walls when compared to bovine derived probiotics.