Arduino MIDI.h library and Timer interrupts

I’m working on a program that uses timer interrupts to determine when to send out MIDI data based on tempo, and nothing seems to be working right. I have a counter that’s incremented in an ISR, and when the counter reaches a certain value a MIDI note is supposed to be sent via MIDI.send, but what’s happening is MIDI.send seems to be just spitting out notes as fast as it can, essentially at the timer interrupt frequency. Does using timer interrupts mess with the serial port transmission somehow?