The 23-year-old striker was jailed for five years after being found guilty of raping a teenage woman in Wales last summer.
The damaging verdict is believed to have caused the Welshman's teammate Brown to launch a verbal attack on the 19-year-old female, branding the victim a "money-grabbing little tramp".
The comments were later deleted and the privacy settings on the Twitter account were tightened.
A spokesman for the League One club said: "The club is aware of a very serious matter regarding comments made through the Twitter account of one of its players. As a result we have launched an inquiry."
The name of the rape victim is also believed to have been illegally announced on the social network site.