I have the same issue. Clicking around in the back office randomly changes the URL to my second subdomain. I have two shops, in the default group, on PS 1.7.4.2.
The funny thing is that if I click on "Categories" in the back office administration repeatedly, every click leads to the other subdomain. And everytime this URL rewrite happens the default selected "Shop", "Shop group" or "All shops" in the top right also changes.
This is real confusing and a bug that should be fixed ASAP.