The VGM format does not support the PC speaker directly, so the AY8910 chip is used as a substitute, which
SonicPlayer does not emulate, but most other players do.
As for the games you mentioned,
try my current DOSBox build which includes updates to PC speaker logging, along with other things not related to VGM logging. I have checked it against the two games you mentioned, and it logs them correctly.
I have not posted that update to the VGM logging code since I was not seriously considering that anybody would actually want to log PC speaker music, and making a new patch against the current DOSBox SVN repository is a major pain. The originally-posted version's PC speaker logging feature worked well enough for the games it was designed to log, namely, Distinctive Software games which use the PC speaker as a fourth voice along with the Tandy 1000's SN76489 chip.