According to Dr Zakir Naik's biography, he started his preaching and founded IRF in 1991.
Even though numerous terrorist incidents took place in India and Bangladesh during the last 26 years, nothing happened during all these years. I.e. even though he was regularly criticized, no one ever linked him with terrorism.
What happened suddenly?
Why has Indian government started a probe against him after 26 years even though he was doing his job as he was doing 26 years ago?
Because the current right wing government wants to stop conversions. Since no substantial evidence could be gathered linking him to terrorist organisations the govt made up a case of foreign donations against him. Such articles with low factual content regularly hit the headlines in indian media outlets.