I remember he used the pirated version of SoundForge, cracked by Radium if I am not mistaken. You can find Radium’s watermark embedded in the wave file
Brian didnt use a PC though, so its possible it was someone downstream that used the cracked soundforge. That version of SoundForge was what I used in college very heavily. I should look at my old sample folder and see how many have the watermark...
IIRC Eno was really into the Yamaha DX7 FM synthesizer around the time he did the Windows 95 sound, it was almost certainly created using that hardware and then later someone mastered it to a wav file (perhaps using a pirated copy of soundforge).
For what it's worth, the DX7 isn't capable of producing most of the sounds heard in the Windows 95 sound. If it was used at all, it would be one out of several synthesizers.
Is your knowledge of Eno's workflow such that you can make this accusation with confidence? I see the demand for the work-product as such that I'm not sure if his output was a file, it may well have been 3.5 seconds of Ampex tape or some other medium.