Here is an interesting article by Christopher Wallis about how the modern western concept of "chakras" came to be: http://www.corespirit.com/real-story-chakras/
The core claim is that the currently prevailing view of the chakras, and of yoga in general, has almost nothing to do with any ancient Indian philosophy. Instead, it is an invention of western occultism of the late 19th century.
What seems to have happened is that people like John Woodroffe translated sanskrit works with little knowledge of the language and huge occultist philosophies in the back of their heads. These were then used in turn by Indian writers who believed that they were talking about actual ancient Indian sources.
According to Wallis, the main differences between the modern systems and actual ancient ideas are:
1. There’s Not Just One Chakra System in The Original Tradition, There Are Many
2. The Chakra Systems are Prescriptive, Not Descriptive
3. The Psychological States Associated with the Chakras are Completely Modern and Western
4. The Seven-Chakra System Popular Today Derives Not From a Scripture, But From a Treatise Written in 1577
5. The Purpose of a Chakra System Is to Function as a Templatefor Nyasa
6. The Seed-Mantras that You Think Go with The Chakras Actually Go with The Elements that Happen to Be Installed in those Chakras
I cannot possibly decide whether there is any truth to that or not. It fits nicely with my personal predilections, and I would be interested to learn more. I put it out there for others to either support or refute.
One thing is for sure: It adds a nice little additional twist to all those right-wing christian warnings about yoga being an ancient demonic force that will insta-turn you into a Hindu...