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According to Dick Brass, a former Microsoft VP, it was internal political sabotage:
“[O]ther Microsoft groups… felt threatened by our success.
“Engineers in the Windows group falsely claimed it made the display go haywire when certain colors were used. The head of Office products said it was fuzzy and gave him headaches. The vice president for pocket devices was blunter: He’d support ClearType and use it, but only if I transferred the program and the programmers to his control. As a result, even though it received much public praise, internal promotion and patents, a decade passed before a fully operational version of ClearType finally made it into Windows.”
(Via Vince Connare’s Facebook.)