Stop using this toilet today. From what you told me the toilet has a crowned bottom or the Water Closet Flange is two heigh. Both of these can result in a leak when the toilet is in use. Chances are that the toilet was installed with a "Can't Leak Wax Ring" the kind with the black plastic collar. These are great rings but the wrong ones to use with a water Closet Flange install properly like you mention. This is one possibility of many. Don't use the toilet. If you or your husband could remove the toilet that would be a good start. Lets start their and wait for the boys to chime in with other ideas.

When I say, being careful, I mean with regards to cleaning products. I eliminated using Lysol Basin, Tub and Tile Cleaner in all three bathrooms, and I try to watch out for drips from the TB brush. We also used travertine in the entryway from our garage, in the laundry room, and two closets off that same entryway. We got a great price on the travertine at the time, and it didn't make sense to us to spend more for a porcelain/ceramic look-alike. We don't baby those floors at all. We wear shoes in the house, and sometimes track in grit and dirt (esp in the spring when we come in from gardening). We slide boxes and laundry baskets across the floor, too. Does the floor look brand new? Probably not. Does it look beat-the-heck up? Definitely not. There are some faint surface scratches I'm sure. Deeper scratches (e.g. from washing machine and/or dryer being moved) I "filled in" using a permanent marker (found brown, beige, tan ones at Staples) and then buffed off any excess with a very fine steel wool pad. To me, the etches looked worse than any scratches. If I can avoid most or remove them if/when they occur, then I am happy we chose travertine for the rooms/areas we did, and would likely use it again.

Just one side note, it was mostly DIY- all of the plumbing and tub installation was done by a plumber. And the plaster walls were resurfaced by a professional. They were pretty bad after removing the tile. And my husband wanted plaster not Sheetrock.

I’ve started planning a bathroom renovation and picked out plumbing, cabinetry, tile etc. the cost is becoming more than I had originally planned. Where should I try and save ‘money’? Cabinetry or flooring? For reference- I designed two vanities with inset cabinetry and chose walker zanger marble flooring. Is it better to find cheaper custom cabinets or different marble/tile floor?