From a Washington Post article after the collapse. Yes they knew for years and ignored the engineering professors.
https://www.washingtonpost.com/archive/politics/1999/12/19/from-why-to-how-at-texas-a38/45ea21bd-f43c-411a-9993-b287c68596f4/
Pulled the important quote
"Since the catastrophe, which occurred a week before Thanksgiving, A&M engineering professor Loren D. Lutes has criticized the stack design, noting that a now-retired A&M colleague had argued for years that the design was "fatally flawed," the Dallas Morning News reported recently. Lutes outlined the flaws in an e-mail message to A&M President Ray Bowen shortly after the collapse, according to the newspaper, which obtained a copy of the message.
Referring to former professor T.J. "Teddy" Hirsch, who retired in the early 1990s, Lutes told Bowen, "Many structural engineering faculty members are well aware of Teddy's unsuccessful attempt to have the design of the stack altered." He said there was a "general agreement" among A&M engineers that "something [is] wrong with the fundamental arrangement of the stack," causing it to be "unstable.""