So has anyone politely asked the establishment the reason for their policy? If not, then do that first. There could be several legitimate reasons, such as alcohol establishment, security reasons, private function in progress, meeting place. It could also be this is not a registered place, or other reasons.
And regarding the places in India, constant racial discrimination is rampant in all cities. The typical scam goes like this: Pretend to provide a "service" to a foreigner, quote a price that is about 5X local price. Then lead them to a dingy suspicious place (especially true if they are the tuk-tuk drivers) so the foreigner becomes lost. Make up some excuse why the fare should now be 10X, and if they foreigner doesn't budge, make THREATS. Here, depending on the situation the scam/thief/police/owner may rob you, rape you, gang attack you, or much worse!
Say there's a vacant motel and you ask to rest. You see a vacant sign and you ask for a single bed. Seeing you are a foreigner their will either: 1) say there's no single beds, only double. Then you ask for double, and they immediately backtrack and say "sorry, me no double beds either!". "But you just said." "No. no. no. I say we only have super-special rooms" "Okay, how much for these rooms?" "$200/night!" "$200 a night?! Not only is that exorbant, but the sign says it's only $20/night right over there!" "No. no. no. you know noting get out!!!"
Or
2) Even though there a empty rooms, they will tell you "No vacancies" (even though right before you people book rooms and after you people book rooms) "Go to XXXX place". So you go to the next establishment, and they say the same sh1t. On and on and on this goes, remember you are a foreign tourist with lots of luggage, and they KNOW you are tired so they EXPLOIT this fact. Finally you go to XXXX place and you find out the same scam as in 1) but only the PRICE is even HIGHER (because they assume, often correctly, that no other establishment will let you stay!)
You can easily see other foreigners get scamed numerous ways. Just as an example. A British man was tricked into missing his flight. Right away another Indian who works for a particular airline (say Deccan) walks up to him and says "I can help you come with me!" So he takes him to a set-up. They then engage in deceptive small talk, collecting data they will later exploit. Then they say oh this flight is "all booked solid (it's never booked solid)" and so he asks "When's the next available flight?" "Oh, not until 3-5 days from now (again a lie)" "But we have this special seat that someone canceled, but it's only a cheap $500 (real indian local price $30)." From their small talk the Indian fraudster knows this man has an important appointment so they reassure him "There's no other way for you to get to XXXX in time, you MUST pay for this!"
Now regarding eating establishments. This is quite common. You find a semi-clean restaurant where you see expats and foreigners like you are coming in and out. So you go in, but you notice the stark treatment received between your caucasian friend, yourself and the Mongoloid (NE). It may seem the white person is being treated well, but shallow perceptions are deceiving. He's being scammed just like you, it's just they think he is RICHER so they play their game differently. What is alarming is how they treat the Mongoloid (e.g. Nagalanders, Manipuris, etc), it's really NASTY! My god, it's really BAD!
It doesn't really matter if there are signs or not, the locals ignore them. If they "like" you (i.e. sucking up to you, or trying to scam you) they will let you in. If they don't like you they will chase you away, and if you're lucky you get to hear a bullsh1t excuse.
So is this just an isolated instances, my personal experience only? No, I've travelled to countless places and nothing is Discriminative as in India.
And I'm definitely not the only one. Go to YouTube - Broadcast Yourself. and you can find videos and testimonies of TENS OF THOUSANDS who've experienced the same and much worse! 
