Hi, if I take lactic acid bacillus over a long term (6-8 months) to reduce IBS or other stomach issues, it has caused acidity and pain in upper stomach region.

Not likely. Typically lactobacillus is taken in a capsule that doesn't even dissolve until it gets through your stomach. You probably have another gastrointestinal issue, possibly H.Pylori in the upper digestive tract responsible for the acidity and pain. See your physician about treatment for this.