Not all VST plugins will run correctly in MusicBee; VST3 for example is not supported, nor of course 64-bit plugins. From what I can see, "Stereo Tool" is a complex plugin and may be taking over control of the built-in equalizer when loaded. I use MB with a single VST (Sonic Anomaly's "Unlimited" compressor/limiter) which works great and doesn't bother the EQ, yet others refuse to work at all. Actually the last free player I've seen with a basically stable VST host was the now abandoned "uLilith." Foobar's own non-native VST host plugins are a "crash-test environment". The lack of free development on these lead me to believe their code is "not for the squeamish."
THAT SAID, maybe others who are using Stereo Tool successfully with MusicBee will post here and share their experience.