Not too sure why it's doing this, but I may have a theory based off something I read on a Sega Megadrive/Genesis emulation forum (the MD/Genesis uses a YM2612, a.k.a. OPN2, same family of FM synth chip).
The OPN chips are based on Yamaha's higher-end FM chips, but instead of a real accumulator-based mixer they time-divide the output of the channels (one slot every 24 clock cycles of the FM chip, apparently). So Anex86 may be implementing a time-division multiplexer (hardware-accurate emulation), while Hoot does actual mixing (high-quality sound).
You might be able to see this happening if you compare the waveforms from Anex86 and Hoot recordings.
From what I also read, 55khz is the proper sampling rate for the OPN-series chips.
By the way, the forum thread is
here, very interesting reading if you like hardcore sound synthesis and electronics. Plus it's very relevant to the PC98 too, as both system's synth chips are related, and quite a bit of their material comes from the OPNA documentation.