The investigation didn't even start because they were suspicious. The team wanted to create a TAS and decided to recreate Groobo as a starting point, then optimise from there. First step of making a TAS was to bruteforce the map generation seed.
And they quickly encountered issues, and it quickly devolved into an investigation of just how "cheated" it was. Partly because for their TAS usecase, they didn't really care if the run was played on multiple versions, as long as it was still a single save file with a single map seed. But I assume it was mostly curiosity at that point.
Groobo's defence was didn't come until near the end of the investigation, and was more or less: "Yes, I did that. But it was all disclosed to the SDA judges, and they allowed it under the rules of that time".