I would suspect that taking probiotics with a fiber supplement would be similar to taking it with a meal. Regardless of how you take it, it would get where it needs to be (there are no detours in our gut). As long as you have a probiotic that is capable of surviving the stomach (strain specific), it should adhere and colonize in the gut.
For whatever reason, those with IBD tend to be less able to colonize with probiotic bacteria. This is why the use of probiotics on a regular basis has been studied for IBD, but results are not consistent. The same is true for j-pouch maintenance.
So, if VSL#3 or other probiotics don't do what you want them to, don't assume you are taking them wrong (unless you are taking them with hot or carbonated liquids/foods). For some of us, they just don't do anything other than cause gas.
Jan