This sounds like mould\damp or stagnant water.
When you lifted the tiles and repaired the leak did you dry out the chipboard floor, and plaster in the ceiling thoroughly?
In most cases when a leak occurs water will soak into the wood and make it damp, and cause a smell.
If the smell goes away when you run the taps, do you notice the same thing when you pour a bucket of water down the drain (and not run the taps)?. Since it might suggest one of the drain traps has failed, and your getting a drain smell coming up through the pipes.
It should dry out if its a concrete floor just a case of turning up the heating for a day or two.
However if you notice the smell goes when you pour water down the drain, its a case of looking at the trap in the shower and sink, to make they are working properly.
I would suggest you get them to check the trap
In most cases if the trap hasnt been fitted correctly, the smell from the soil stack (main drain) rises up out of the plug hole, hence why if you pour water down it, the smell appears to disappear for a short time.
If there was damp under the floor a month would have cleared it, so I think its a case of getting the plumbers back and check the trap is stopping smells rising from the drain.
Please let me know if I can be of any further assistance.
Appreciate if you can log back in and rate the service using the start rating of the page, so I can receive payment from JA.
As always should you have any follow up quesitons please let me know.