We had a new bathtub and all new plumbing installed (including new toilet) last March. We then had new flooring installed (glued down and sealed to the tub as normal). We didn't care for the flooring so a month later we got another new one (Tarkett) installed. This is a "floating floor" lino so it isn't glued down. Anyway... a few weeks ago our floor boards started to squeak between the toilet and the tub (about 2 feet) and is getting worse. We can lift the existing floating floor and we don't see any water damage or leaks. Even when you sit on the toilet now the floor beside it squeaks. What could be causing this and how can this annoying squeak be stopped?

Did you have any subfloor replaced due to rot around the tub/toilet area?

Usually when a floor squeaks its because the joist or subfloor was swollen due to moisture. Over time the wood "dries out". The fastener, usually a nail, was nailed straight into the subfloor into the joist. When everything dries out, the sub floor rides up and down on the nail because the subfloor is no longer tight to the joist.
It is better to use subfloor adhesive and install the nail at an angle or use the proper length screw.

If you can find the joists around the tub/toilet area try to screw down the subfloor with 3" screws.

Yes we did replace the subfloor around the toilet as the tub and toilet both had leaked before and it was all rotten. So you think the newer subfloor needs to be nailed down again to the joists? How do you recommend we do this. We do have the "floating" lino floor which can easily be lifted. Do you think we could just put in screws in through the lino that was originally glued down to the joists and then just relay our new lino overtop of it? Of course we would make sure the screw heads are down far enough to not tear the new lino.

Yes you can screw right threw the existing "old" vinyl into the joist if you know where they're at. Hopefully this will help. Its worth a try.
Good idea on driving the heads below the vinyl.