Hello JCastro - this sounds familiar to my early days with Astroberry. For me, it turned out to be a combination of a known hardware conflict between the USB3 chip and the 2.4GHz radio for wifi on my rpi4 (I know you're rpi3) and also that I was not using a decent powered USB hub (I had plugged everything into my 4 ports on the rpi).
Have you turned on your debugging logs in EKOS? The devs in this forum are quite good at reading these and discovering configuration conflicts or bugs.
Also you could look through your system logs to see if there are excessive USB resets or conflicts/timeouts. From a command prompt you could type "sudo dmesg | grep -i usb" (the vertical line is a pipe symbol usually shift + \ it's not the letter "i")