but first experiment with a 2 foot level placed in the area near the floor colar. see if the floor is level in that area.
What you need to ensure is that your tile work is as close to the floor flange as possible. sometimes the tile work barely goes under the foundation of the base of the toilet and when pressure is applied the base can crack the tile because there is not enough of the tile to sit on.
If shims are needed to level the area, then use something like pieces of ceramic tile, pieces of vinyl tile or anything other than WOOD. Wood will rot.
Once its shimed up, then 100% silicon caulk it.
But, where many people mess up is in the tightening of the base bolts. BE SURE AND SCRAPE AWAY ALL THE OLD WAX RING AND INSTALL NEW THE PROPER WAY.
Set the flange bolts in the colar and place a drinking straw over the bolts so they stick up higher and you can much easier align the bolts with the base holes.
Set the base down firmly and alternately press with one hand on the stool to seat it down. Now alternately tighten the nuts down on the bolt. DO NOT OVER TIGHTEN AND THEREFORE BREAK THE BASE. Run them down, then sit on the comode and shift back and forth. Tighten again carefully, Take up the slack and then set the level on the seat and check for levelness. you can carefully adjust levelness by tightening either one of the nuts down more. Do not run them down like auto lug nuts. When level sit on the base again and apply weight. turn each nut the same amount of turns to take up any more slack. Check for levelness.
When done, caulk around base, let it sit and you should be OK.