I have two Magento websites in the same domain, store.com and us.store.com.
For 24 hours I can't login in the backend. Only If I use a plugin browser like anonimoX, which changes my IP the login works. So I think it is a problem witht cookies.
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System > Configuration > Web > Session Cookie Management and set a different cookie domain for your two websites.
store.com(make sure it is NOT
Flush your cache (both Magento and browser) and try again, it should fix it.