I made a thread on this a year ago in the wishlist forum too. I was in the exact same boat as you, I bought a hifi DAC, but the first second of every song was being cut off. I made a thread in this forum asking for an option to include second(s) silence to the start of every thread. But it was just getting ignored. No one replied to it. Eventually, I just asked Phred to delete the thread, and I stopped using Musicbee and switched to Foobar.
The reason there's a silence is because the DAC needs a second to initialize. There are players out there like Jriver that just take account for DACs automatically, and there's no silence at the start of tracks. For Foobar, there's the DSP "Affix silence". I set it up to play a 500 milliseconds silence before starting every track, and it works well.
Glad it got attention though, maybe I can go back to Musicbee. Used it for years and enjoyed it.
Also, I wanted to add, 100ms is not enough. Try 500ms. It might depend on the DAC you're using though.
Also, please add support for ASIO and/or include an option for silence at the start of tracks