I just started taking VSL #3 and have noticed an increase in gas/bloating. I'm getting up 4-5 times at night because of the gas. Is this common when starting probiotics? Will these side effects eventually go away when my body gets used to the extra bacteria in my system?

Sometimes it takes a while for your body to become used to the probiotic and you will get the symptoms you describe. And too, some folks cut back on the dose of VSL#3 and see what works best.

Yes I'd use a low dose for a while. If you're on more than 1 sachet a day then try dropping back to 1 only. If you're only on 1 then I'd think about trying a half sachet a day.